Cyanine dye compounds

ABSTRACT

Cyanine dye compounds having a negatively charged substituent that are nucleic acid stains, particularly for fluorescent staining of DNA, including compounds having the formula 
                         
wherein W forms one or two fused 5- or 6-membered aromatic rings, α has a value of 0 or 1, n has a value of 0, or 1, X is O, S, or Se, and D is a pyridinium, or quinolinium moiety, provided that the compound has at least one negatively charged substituent.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. Ser. No. 11/005,860, filed Dec.6, 2004, which claims priority to U.S. Ser. No. 60/527,234, filed Dec.5, 2003; and U.S. Ser. No. 60/554,472 filed Mar. 18, 2004, whichdisclosures are herein incorporated by reference.

FIELD OF THE INVENTION

The present invention relates to cyanine compounds useful for stainingnucleic acids, including DNA. The invention has applications in thefields of molecular biology, particularly with respect tofluorescence-based assays.

BACKGROUND OF THE INVENTION

In selected fields of life sciences research, including for examplebiological, biomedical, genetic, fermentation, aquaculture,agricultural, forensic and environmental research, there may often occurthe need to identify nucleic acids, qualitatively and quantitatively, inpure solutions and in biological samples. Such applications may benefitfrom fast, sensitive, and selective methodologies for detecting and/orquantifying nucleic acids of interest.

In particular, it may be helpful in some research venues to providemolecular species that at least somewhat selectively stain DNA even inthe presence of RNA. That is, the probe or reagent may permit theresearcher to distinguish DNA present in a sample from RNA in the samesample.

SUMMARY

Embodiments of the present invention provide nucleic acid reportercompounds having at least one negatively charged substituent at aphysiological pH. These reporter compounds find use as nucleic acidstains, particularly for the fluorescent detection/quantitation of DNA.

In one embodiment, the nucleic acid reporter molecules have the formula:

wherein W represents the atoms necessary to form one or two fusedsubstituted 5- or 6-membered aromatic rings or one or two unsubstituted5- or 6-membered aromatic rings. In one aspect W comprises —C, —CR¹, or—N(R²)_(β); wherein β is 0 or 1, provided that α+β=1; and each R¹ isindependently hydrogen, a reactive group, a carrier molecule, a solidsupport, carboxy, sulfo, phosphate, phosphonate, amino, hydroxy,substituted aryl, unsubstituted aryl, substituted heteroaryl,unsubstituted heteroaryl, trifluoromethyl, halogen, substituted alkyl,unsubstituted alkyl, alkoxy, substituted alkylamino, unsubstitutedalkylamino, substituted dialkylamino, or unsubstituted dialkylamino.

R² is a substituted alkyl, unsubstituted alkyl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroalkyl, unsubstitutedheteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy, hydroxyalkyl,sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino, dialkylamino, ortrialkylammonium.

In one aspect at least one of R¹ and R² is a negatively charged moiety,which are selected from the group consisting of sulfo, carboxy,phosphate, phosphonate, an alkyl group substituted by sulfo, an alkylgroup substituted by a carboxy, an alkyl group substituted by phosphate,or an alkyl group substituted by phosphonate.

α is 0 or 1; n is 0 or 1; X is O, S, or Se; and

D is a substituted pyridinium, unsubstituted pyridinium, substitutedquinolinium, or unsubstituted quinolinium moiety.

In an exemplary embodiment D has the formula:

wherein R³, R⁴, R⁵, and R⁶ are independently hydrogen, substitutedalkyl, unsubstituted alkyl, substituted heteroalkyl, unsubstitutedheteroalkyl, substituted aryl, unsubstituted aryl, substitutedarylalkyl, unsubstituted arylalkyl, substituted heteroarylalkyl;unsubstituted heteroarylalkyl, substituted heteroaryl, unsubstitutedheteroaryl, substituted cycloalkyl, unsubstituted cycloalkyl,substituted heterocycloalkyl, unsubstituted heterocycloalkyl, halogen,alkoxy, substituted alkylamino, unsubstituted alkylamino, substitutedalkylthio, unsubstituted alkylthio, reactive group, solid support, orcarrier molecule. Alternatively, a member selected from R⁵ incombination with R⁶; R⁴ in combination with R⁵; R⁴ in combination withR³; R⁴ in combination with R⁶; R³ in combination with R⁶, together withthe atoms to which they are joined, form a ring which is a 5-, 6- or7-membered heterocycloalkyl, a substituted 5-, 6- or 7-memberedheterocycloalkyl, a 5-, 6- or 7-membered cycloalkyl, a substituted 5-,6- or 7-membered cycloalkyl, a 5-, 6- or 7-membered heteroaryl, asubstituted 5-, 6- or 7-membered heteroaryl, a 5-, 6- or 7-membered arylor a substituted 5-, 6- or 7-membered aryl.

In an exemplary embodiment, the present reporter molecules have theformula:

-   -   or the formula

wherein each R^(1a)R^(1b) are independently hydrogen, carboxy, sulfo,phosphate, phosphonate, amino, hydroxyl, trifluoromethyl, halogen,alkyl, substituted alkyl, alkoxy, alkylamino, substituted alkylamino,dialkylamino, substituted dialkylamino, fused benzene, substituted fusedbenzene, trifluomethyl, halogen, reactive group, solid support orcarrier molecule.

Additional embodiments of the present invention provide methods ofdetecting the presence or absence of nucleic acid, including method fordetecting the presence or absence of DNA in the presence of RNA. Thepresent methods comprise:

-   -   a. combining a present nucleic acid reporter molecule with the        sample to prepare a labeling mixture;    -   b. incubating the labeling mixture for a sufficient amount of        time for the nucleic acid reporter molecule to associate with        nucleic acid in the sample to form an incubated mixture;    -   c. illuminating the incubated sample with an appropriate        wavelength to form an illuminated mixture; and,    -   d. observing the illuminated mixture whereby the presence or        absence of the nucleic acid in a sample is detected.

Also provided is a staining solution comprising a present nucleic acidreporter molecule and a detergent. The detergent is typically present inan aqueous solution at a concentration from about 0.01% to about 0.5%.Detergents include CHAPTS, Triton-X, SDS and Tween 20.

Further embodiments provide complexes of the present compoundsnon-covalently associated with nucleic acid and compositions comprisinga present compound and a sample. In one aspect the sample comprisesbiological fluids, buffer solutions, live cells, fixed cells, eukaryoticcells, prokaryotic cells, nucleic acid polymers, nucleotides,nucleosides, a polymeric gel or tissue sections. In a further aspect thesample is present in an aqueous solution, in or on a microarray or amicrowell plate.

Additional embodiments of the present invention provide kits for thedetection of nucleic acid, wherein the kit comprises any compound of thepresent invention. In a further embodiment, the kits compriseinstructions for the detection of nucleic acid, particularlyinstructions for the detection of DNA in the presence of RNA. In yetanother further embodiment, the kits comprises at least one componentthat is a sample preparation reagent, a buffering agent, an organicsolvent, an aqueous nucleic acid reporter molecule dilution buffer,nucleic acid control, or an additional detection reagent.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1: A plot showing the fluorescence emission intensity of Compound25 bound to rRNA and DNA (calf thymus), respectively, with excitation at500 nm, as described in Example 31.

FIG. 2: A plot showing the intensity of the fluorescent signal fromCompound 25 when bound to different concentrations of rRNA and DNA (calfthymus) in solution. Compound 25 exhibits little to no detectablefluorescent signal in the presence of RNA, even at a concentration of 10mg/ml, as described in Example 32.

FIG. 3: A plot showing the intensity of the fluorescent signal fromCompound 25 when bound to different concentrations of DNA, RNA orRNA+DNA in solution. FIG. 3 indicates that in solution Compound 25either does not bind RNA or binds RNA with little to no fluorescentsignal intensity which is confirmed by the same fluorescence intensitysignal for the RNA+DNA as for the corresponding DNA concentration, asdescribed in Example 33.

FIG. 4: A plot showing the intensity of the fluorescent signal fromCompound 25 when bound to different concentrations of DNA and RNA+DNA,respectively, in solution. These results indicate that Compound 25, insolution, demonstrates an ability to selectively associate with DNA inthe presence of varying concentrations of RNA, as described in Example34.

FIG. 5: A plot showing a titration of Compound 25 when bound to DNA orRNA in solution. These results show little to no fluorescent signal inthe presence of RNA, and a detectable signal in the presence of DNA, asdescribed in Example 35.

FIG. 6: A black and white image showing the detection of single anddouble stranded DNA immobilized in a microarray, using Compound 5. Theseresults indicate that Compound 5 is more selective for double strandedDNA compared to single stranded DNA when the nucleic acid is immobilizedon solid support. See Example 36.

FIG. 7: A black and white image showing the detection of hybridized DNAimmobilized in a microarray, by illumination of a fluorescent-labeledhybridization probe. These results show hybridization of the probe toDNA that is 100% complementary (middle rows 3 and 4) and partiallycomplimentary (top rows 1 and 2), but no hybridization tonon-complementary DNA (bottom rows 5 and 6), as described in Example 37.

FIG. 8: A black and white image showing the relative fluorescenceintensity of single-stranded and hybridized DNA immobilized in amicroarray and stained using Compound 5. Hybridized (double-stranded)DNA (in rows 1-4) exhibits brighter fluorescence than single-strandedDNA (in bottom rows 5 and 6), as described in Example 37.

DETAILED DESCRIPTION OF THE INVENTION Definitions

Before describing the present invention in detail, it is to beunderstood that this invention is not limited to specific compositionsor process steps, as such may vary. It must be noted that, as used inthis specification and the appended claims, the singular form “a”, “an”and “the” include plural referents unless the context clearly dictatesotherwise. Thus, for example, reference to “a compound” includes aplurality of compounds and reference to “a nucleic acid” includes aplurality of nucleic acids and the like.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention is related. The following terms aredefined for the purposes of understanding the present disclosure.

Certain compounds of the present invention can exist in unsolvated formsas well as solvated forms, including hydrated forms. In general, thesolvated forms are equivalent to unsolvated forms and are encompassedwithin the scope of the present invention. Certain compounds of thepresent invention may exist in multiple crystalline or amorphous forms.In general, all physical forms are equivalent for the uses contemplatedby the present invention and are intended to be within the scope of thepresent invention.

Certain compounds of the present invention possess asymmetric carbonatoms (optical centers) or double bonds; the racemates, diastereomers,geometric isomers and individual isomers are encompassed within thescope of the present invention.

The compounds described herein may be prepared as a single isomer (e.g.,enantiomer, cis-trans, positional, diastereomer) or as a mixture ofisomers. In a preferred embodiment, the compounds are prepared assubstantially a single isomer. Methods of preparing substantiallyisomerically pure compounds are known in the art. For example,enantiomerically enriched mixtures and pure enantiomeric compounds canbe prepared by using synthetic intermediates that are enantiomericallypure in combination with reactions that either leave the stereochemistryat a chiral center unchanged or result in its complete inversion.Alternatively, the final product or intermediates along the syntheticroute can be resolved into a single stereoisomer. Techniques forinverting or leaving unchanged a particular stereocenter, and those forresolving mixtures of stereoisomers are well known in the art and it iswell within the ability of one of skill in the art to choose andappropriate method for a particular situation. See, generally, Furnisset al. (eds.), VOGEL'S ENCYCLOPEDIA OF PRACTICAL ORGANIC CHEMISTRY5^(TH) ED., Longman Scientific and Technical Ltd., Essex, 1991, pp.809-816; and Heller, Acc. Chem. Res. 23:128 (1990).

The compounds disclosed herein may also contain unnatural proportions ofatomic isotopes at one or more of the atoms that constitute suchcompounds. For example, the compounds may be radiolabeled withradioactive isotopes, such as for example tritium (³H), iodine-125(¹²⁵I) or carbon-14 (¹⁴C). All isotopic variations of the compounds ofthe present invention, whether radioactive or not, are intended to beencompassed within the scope of the present invention.

Where a disclosed compound includes a conjugated ring system, resonancestabilization may permit a formal electronic charge to be distributedover the entire molecule. While a particular charge may be depicted aslocalized on a particular ring system, or a particular heteroatom, it iscommonly understood that a comparable resonance structure can be drawnin which the charge may be formally localized on an alternative portionof the compound.

Selected compounds having a formal electronic charge may be shownwithout an appropriate biologically compatible counterion. Such acounterion serves to balance the positive or negative charge present onthe compound. As used herein, a substance that is biologicallycompatible is not toxic as used, and does not have a substantiallydeleterious effect on biomolecules. Examples of negatively chargedcounterions include, among others, chloride, bromide, iodide, sulfate,alkanesulfonate, arylsulfonate, phosphate, perchlorate,tetrafluoroborate, tetraarylboride, nitrate and anions of aromatic oraliphatic carboxylic acids. Preferred counterions may include chloride,iodide, perchlorate and various sulfonates. Examples of positivelycharged counterions include, among others, alkali metal, or alkalineearth metal ions, ammonium, or alkylammonium ions.

Where substituent groups are specified by their conventional chemicalformulae, written from left to right, they equally encompass thechemically identical substituents, which would result from writing thestructure from right to left, e.g., —CH₂O— is intended to also recite—OCH₂—.

The term “acyl” or “alkanoyl” by itself or in combination with anotherterm, means, unless otherwise stated, a stable straight or branchedchain, or cyclic hydrocarbon radical, or combinations thereof,consisting of the stated number of carbon atoms and an acyl radical onat least one terminus of the alkane radical. The “acyl radical” is thegroup derived from a carboxylic acid by removing the —OH moietytherefrom.

The term “affinity” as used herein refers to the strength of the bindinginteraction of two molecules, such as a nucleic acid polymer and anintercalating agent or a positively charged moiety and a negativelycharged moiety.

The term “alkyl,” by itself or as part of another substituent means,unless otherwise stated, a straight or branched chain, or cyclichydrocarbon radical, or combination thereof, which may be fullysaturated, mono- or polyunsaturated and can include divalent(“alkylene”) and multivalent radicals, having the number of carbon atomsdesignated (i.e. C₁-C₁₀ means one to ten carbons). Examples of saturatedhydrocarbon radicals include, but are not limited to, groups such asmethyl, ethyl, n-propyl, isopropyl, n-butyl, t-butyl, isobutyl,sec-butyl, cyclohexyl, (cyclohexyl)methyl, cyclopropylmethyl, homologsand isomers of, for example, n-pentyl, n-hexyl, n-heptyl, n-octyl, andthe like. An unsaturated alkyl group is one having one or more doublebonds or triple bonds. Examples of unsaturated alkyl groups include, butare not limited to, vinyl, 2-propenyl, crotyl, 2-isopentenyl,2-(butadienyl), 2,4-pentadienyl, 3-(1,4-pentadienyl), ethynyl, 1- and3-propynyl, 3-butynyl, and the higher homologs and isomers. The term“alkyl,” unless otherwise noted, is also meant to include thosederivatives of alkyl defined in more detail below, such as“heteroalkyl.” Alkyl groups that are limited to hydrocarbon groups aretermed “homoalkyl”.

Exemplary alkyl groups of use in the present invention contain betweenabout one and about twenty five carbon atoms (e.g. methyl, ethyl and thelike). Straight, branched or cyclic hydrocarbon chains having eight orfewer carbon atoms will also be referred to herein as “lower alkyl”. Inaddition, the term “alkyl” as used herein further includes one or moresubstitutions at one or more carbon atoms of the hydrocarbon chainfragment. The term “amino” or “amine group” refers to the group —NR′R″(or NRR′R″) where R, R′ and R″ are independently selected from the groupconsisting of hydrogen, alkyl, substituted alkyl, aryl, substitutedaryl, aryl alkyl, substituted aryl alkyl, heteroaryl, and substitutedheteroaryl. A substituted amine being an amine group wherein R′ or R″ isother than hydrogen. In a primary amino group, both R′ and R″ arehydrogen, whereas in a secondary amino group, either, but not both, R′or R″ is hydrogen. In addition, the terms “amine” and “amino” caninclude protonated and quaternized versions of nitrogen, comprising thegroup —NRR′R″ and its biologically compatible anionic counterions.

The term “aryl” as used herein refers to cyclic aromatic carbon chainhaving twenty or fewer carbon atoms, e.g., phenyl, naphthyl, biphenyl,and anthracenyl. One or more carbon atoms of the aryl group may also besubstituted with, e.g., alkyl; aryl; heteroaryl; a halogen; nitro;cyano; hydroxyl, alkoxyl or aryloxyl; thio or mercapto, alkyl-, orarylthio; amino, alkylamino, arylamino, dialkyl-, diaryl-, orarylalkylamino; aminocarbonyl, alkylaminocarbonyl, arylaminocarbonyl,dialkylaminocarbonyl, diarylaminocarbonyl, or arylalkylaminocarbonyl;carboxyl, or alkyl- or aryloxycarbonyl; aldehyde; aryl- oralkylcarbonyl; iminyl, or aryl- or alkyliminyl; sulfo; alkyl- oralkylcarbonyl; iminyl, or aryl- or alkyliminyl; sulfo; alkyl- orarylsulfonyl; hydroximinyl, or aryl- or alkoximinyl. In addition, two ormore alkyl or heteroalkyl substituents of an aryl group may be combinedto form fused aryl-alkyl or aryl-heteroalkyl ring systems (e.g.,tetrahydronaphthyl). Substituents including heterocyclic groups (e.g.,heteroaryloxy, and heteroaralkylthio) are defined by analogy to theabove-described terms.

The terms “alkoxy,” “alkylamino” and “alkylthio” (or thioalkoxy) areused in their conventional sense, and refer to those alkyl groupsattached to the remainder of the molecule via an oxygen atom, an aminogroup, or a sulfur atom, respectively.

The term “heteroalkyl,” by itself or in combination with another term,means, unless otherwise stated, a straight or branched chain, or cycliccarbon-containing radical, or combinations thereof, consisting of thestated number of carbon atoms and at least one heteroatom selected fromthe group consisting of O, N, Si, P, S, and Se and wherein the nitrogen,phosphorous, sulfur, and selenium atoms are optionally oxidized, and thenitrogen heteroatom is optionally be quaternized. The heteroatom(s) O,N, P, S, Si, and Se may be placed at any interior position of theheteroalkyl group or at the position at which the alkyl group isattached to the remainder of the molecule. Examples include, but are notlimited to, —CH₂—CH₂—O—CH₃, —CH₂—CH₂—NH—CH₃, —CH₂—CH₂—N(CH₃)—CH₃,—CH₂—S—CH₂—CH₃, —CH₂—CH₂, —S(O)—CH₃, —CH₂—CH₂—S(O)₂—CH₃, —CH═CH—O—CH₃,—Si(CH₃)₃, —CH₂—CH═N—OCH₃, and —CH═CH—N(CH₃)—CH₃. Up to two heteroatomsmay be consecutive, such as, for example, —CH₂—NH—OCH₃ and—CH₂—O—Si(CH₃)₃. Similarly, the term “heteroalkylene” by itself or aspart of another substituent means a divalent radical derived fromheteroalkyl, as exemplified, but not limited by, —CH₂—CH₂—S—CH₂—CH₂— and—CH₂—S—CH₂—CH₂—NH—CH₂—. For heteroalkylene groups, heteroatoms can alsooccupy either or both of the chain termini (e.g., alkyleneoxy,alkylenedioxy, alkyleneamino, alkylenediamino, and the like). Stillfurther, for alkylene and heteroalkylene linking groups, no orientationof the linking group is implied by the direction in which the formula ofthe linking group is written. For example, the formula —C(O)₂R′—represents both —C(O)₂R′— and —R′C(O)₂—.

The terms “cycloalkyl” and “heterocycloalkyl”, by themselves or incombination with other terms, represent, unless otherwise stated, cyclicversions of “alkyl” and “heteroalkyl”, respectively. Additionally, forheterocycloalkyl, a heteroatom can occupy the position at which theheterocycle is attached to the remainder of the molecule. Examples ofcycloalkyl include, but are not limited to, cyclopentyl, cyclohexyl,1-cyclohexenyl, 3-cyclohexenyl, cycloheptyl, and the like. Examples ofheterocycloalkyl include, but are not limited to,1-(1,2,5,6-tetrahydropyridyl), 1-piperidinyl, 2-piperidinyl,3-piperidinyl, 4-morpholinyl, 3-morpholinyl, tetrahydrofuran-2-yl,tetrahydrofuran-3-yl, tetrahydrothien-2-yl, tetrahydrothien-3-yl,1-piperazinyl, 2-piperazinyl, and the like.

The term “aryl” means, unless otherwise stated, a polyunsaturated,aromatic moiety that can be a single ring or multiple rings (preferablyfrom 1 to 3 rings), which are fused together or linked covalently. Theterm “heteroaryl” refers to aryl groups (or rings) that contain from oneto four heteroatoms selected from N, O, S, and Se, wherein the nitrogen,sulfur, and selenium atoms are optionally oxidized, and the nitrogenatom(s) are optionally quaternized. A heteroaryl group can be attachedto the remainder of the molecule through a heteroatom. Non-limitingexamples of aryl and heteroaryl groups include phenyl, 1-naphthyl,2-naphthyl, 4-biphenyl, 1-pyrrolyl, 2-pyrrolyl, 3-pyrrolyl, 3-pyrazolyl,2-imidazolyl, 4-imidazolyl, pyrazinyl, 2-oxazolyl, 4-oxazolyl,2-phenyl-4-oxazolyl, 5-oxazolyl, 3-isoxazolyl, 4-isoxazolyl,5-isoxazolyl, 2-thiazolyl, 4-thiazolyl, 5-thiazolyl, 2-furyl, 3-furyl,2-thienyl, 3-thienyl, 2-pyridyl, 3-pyridyl, 4-pyridyl, 2-pyrimidyl,4-pyrimidyl, 5-benzothiazolyl, purinyl, 2-benzimidazolyl, 5-indolyl,1-isoquinolyl, 5-isoquinolyl, 2-quinoxalinyl, 5-quinoxalinyl,3-quinolyl, tetrazolyl, benzo[b]furanyl, benzo[b]thienyl,2,3-dihydrobenzo[1,4]dioxin-6-yl, benzo[1,3]dioxol-5-yl and 6-quinolyl.Substituents for each of the above noted aryl and heteroaryl ringsystems are selected from the group of acceptable substituents describedbelow.

For brevity, the term “aryl” when used in combination with other terms(e.g., aryloxy, arylthioxy, arylalkyl) includes both aryl and heteroarylrings as defined above. Thus, the term “arylalkyl” is meant to includethose radicals in which an aryl group is attached to an alkyl group(e.g., benzyl, phenethyl, pyridylmethyl and the like) including thosealkyl groups in which a carbon atom (e.g., a methylene group) has beenreplaced by, for example, an oxygen atom (e.g., phenoxymethyl,2-pyridyloxymethyl, 3-(1-naphthyloxy)propyl, and the like).

Each of the above terms (e.g., “alkyl,” “heteroalkyl,” “aryl” and“heteroaryl”) includes both substituted and unsubstituted forms of theindicated radical. Preferred substituents for each type of radical areprovided below.

Substituents for the alkyl and heteroalkyl radicals (including thosegroups often referred to as alkylene, alkenyl, heteroalkylene,heteroalkenyl, alkynyl, cycloalkyl, heterocycloalkyl, cycloalkenyl, andheterocycloalkenyl) are generically referred to as “alkyl groupsubstituents,” and they can be one or more of a variety of groupsselected from, but not limited to: —OR′, ═O, ═NR′, ═N—OR′, —NR′R″, —SR′,-halogen, —SiR′R″R′″, —OC(O)R′, —C(O) R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″,—NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″,—NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —CN and—NO₂ in a number ranging from zero to (2m′+1), where m′ is the totalnumber of carbon atoms in such radical. R′, R″, R′″ and R″″ eachpreferably independently refer to hydrogen, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted aryl, e.g., aryl substitutedwith 1-3 halogens, substituted or unsubstituted alkyl, alkoxy orthioalkoxy groups, or arylalkyl groups. When a compound includes morethan one R group, for example, each of the R groups is independentlyselected as are each R′, R″, R′″ and R″″ groups when more than one ofthese groups is present. When R′ and R″ are attached to the samenitrogen atom, they can be combined with the nitrogen atom to form a 5-,6-, or 7-membered ring. For example, —NR′R″ is meant to include, but notbe limited to, 1-pyrrolidinyl and 4-morpholinyl. From the abovediscussion of substituents, one of skill in the art will understand thatthe term “alkyl” is meant to include groups including carbon atoms boundto groups other than hydrogen groups, such as haloalkyl (e.g., —CF₃ and—CH₂CF₃) and acyl (e.g., —C(O)CH₃, —C(O)CF₃, —C(O)CH₂OCH₃, and thelike).

Similar to the substituents described for the alkyl radical,substituents for the aryl and heteroaryl groups are generically referredto as “aryl group substituents.” The substituents are selected from, forexample: halogen, —OR′, ═O, ═NR′, ═N—OR′, —NR′R″, —SR′, -halogen,—SiR′R″R′″, —OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″,—NR″C(O)R′, —NR′—C(O)NR″R′″, —NR″C(O)₂R′, —NR—C(NR′R″R′″)═NR″″,—NR—C(NR′R″)═NR′″, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —CN and—NO₂, —R′, —N₃, —CH(Ph)₂, fluoro(C₁-C₄)alkoxy, and fluoro(C₁-C₄)alkyl,in a number ranging from zero to the total number of open valences onthe aromatic ring system; and where R′, R″, R′″ and R″″ are preferablyindependently selected from hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted aryl and substituted or unsubstituted heteroaryl. When acompound includes more than one R group, for example, each of the Rgroups is independently selected as are each R′, R″, R′″ and R″″ groupswhen more than one of these groups is present. In the schemes thatfollow, the symbol X represents “R” as described above.

Two of the substituents on adjacent atoms of the aryl or heteroaryl ringmay optionally be replaced with a substituent of the formula-T-C(O)—(CRR′)_(q)—U—, wherein T and U are independently —NR—, —O—,—CRR′— or a single bond, and q is an integer of from 0 to 3.Alternatively, two of the substituents on adjacent atoms of the aryl orheteroaryl ring may optionally be replaced with a substituent of theformula -A-(CH₂)_(r)—B—, wherein A and B are independently —CRR′—, —O—,—NR—, —S—, —S(O)—, —S(O)₂—, —S(O)₂NR′— or a single bond, and r is aninteger of from 1 to 4. One of the single bonds of the new ring soformed may optionally be replaced with a double bond. Alternatively, twoof the substituents on adjacent atoms of the aryl or heteroaryl ring mayoptionally be replaced with a substituent of the formula—(CRR′)_(s)—X—(CR″R′″)_(d)—, where s and d are independently integers offrom 0 to 3, and X is —O—, —NR′—, —S—, —S(O)—, —S(O)₂—, or —S(O)₂NR′—.The substituents R, R′, R″ and R′″ are preferably independently selectedfrom hydrogen or substituted or unsubstituted (C₁-C₆)alkyl.

As used herein, the term “heteroatom” includes oxygen (O), nitrogen (N),sulfur (S), phosphorus (P), silicon (Si), and selenium (Se).

The term “amino” or “amine group” refers to the group —NR′R″ (orN⁺RR′R″) where R, R′ and R″ are independently selected from the groupconsisting of hydrogen, alkyl, substituted alkyl, aryl, substitutedaryl, aryl alkyl, substituted aryl alkyl, heteroaryl, and substitutedheteroaryl. A substituted amine being an amine group wherein R′ or R″ isother than hydrogen. In a primary amino group, both R′ and R″ arehydrogen, whereas in a secondary amino group, either, but not both, R′or R″ is hydrogen. In addition, the terms “amine” and “amino” caninclude protonated and quaternized versions of nitrogen, comprising thegroup —N⁺RR′R″ and its biologically compatible anionic counterions.

The term “aqueous solution” as used herein refers to a solution that ispredominantly water and retains the solution characteristics of water.Where the aqueous solution contains solvents in addition to water, wateris typically the predominant solvent.

The term “Carboxyalkyl” as used herein refers to a group having thegeneral formula —(CH₂)_(n)COOH wherein n is 1-18.

The term “carrier molecule” as used herein refers to a biological or anon-biological component that is covalently bonded to a compound of thepresent invention. Such components include, but are not limited to, anamino acid, a peptide, a protein, a polysaccharide, a nucleoside, anucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, adrug, a hormone, a lipid, a lipid assembly, a synthetic polymer, apolymeric microparticle, a biological cell, a virus and combinationsthereof.

The term “complex” as used herein refers to the association of two ormore molecules, usually by non-covalent bonding.

The term “cyanine dye” as used herein refers to a fluorogenic compoundthat comprises 1) a substituted or unsubstituted benzazolium moiety, 2)a polymethine bridge and 3) a substituted or unsubstituted pyridinium orquinolinium moiety. These monomer or dye moieties are capable of forminga non-covalent complex with nucleic acid and demonstrating an increasedfluorescent signal after formation of the nucleic acid-dye complex.

The term “detectable response” as used herein refers to a change in oran occurrence of, a signal that is directly or indirectly detectableeither by observation or by instrumentation. Typically, the detectableresponse is an optical response resulting in a change in the wavelengthdistribution patterns or intensity of absorbance or fluorescence or achange in light scatter, fluorescence lifetime, fluorescencepolarization, or a combination of the above parameters.

The term “kit” as used refers to a packaged set of related components,typically one or more compounds or compositions.

The term “Linker” or “L”, as used herein, refers to a single covalentbond or a series of stable covalent bonds incorporating 1-20 nonhydrogenatoms selected from the group consisting of C, N, O, S and P thatcovalently attach the fluorogenic or fluorescent compounds to anothermoiety such as a chemically reactive group or a biological andnon-biological component.

Exemplary linking members include a moiety that includes —C(O)NH—,—C(O)O—, —NH—, —S—, —O—, and the like. A “cleavable linker” is a linkerthat has one or more cleavable groups that may be broken by the resultof a reaction or condition. The term “cleavable group” refers to amoiety that allows for release of a portion, e.g., a fluorogenic orfluorescent moiety, of a conjugate from the remainder of the conjugateby cleaving a bond linking the released moiety to the remainder of theconjugate. Such cleavage is either chemical in nature, or enzymaticallymediated. Exemplary enzymatically cleavable groups include natural aminoacids or peptide sequences that end with a natural amino acid.

In addition to enzymatically cleavable groups, it is within the scope ofthe present invention to include one or more sites that are cleaved bythe action of an agent other than an enzyme. Exemplary non-enzymaticcleavage agents include, but are not limited to, acids, bases, light(e.g., nitrobenzyl derivatives, phenacyl groups, benzoin esters), andheat. Many cleaveable groups are known in the art. See, for example,Jung et al., Biochem. Biophys. Acta, 761: 152-162 (1983); Joshi et al.,J. Biol. Chem., 265: 14518-14525 (1990); Zarling et al., J. Immunol.,124: 913-920 (1980); Bouizar et al., Eur. J. Biochem., 155: 141-147(1986); Park et al., J. Biol. Chem., 261: 205-210 (1986); Browning etal., J. Immunol., 143: 1859-1867 (1989). Moreover a broad range ofcleavable, bifunctional (both homo- and hetero-bifunctional) spacer armsare commercially available.

An exemplary cleavable group, an ester, is cleavable group that may becleaved by a reagent, e.g. sodium hydroxide, resulting in acarboxylate-containing fragment and a hydroxyl-containing product.

The linker can be used to attach the compound to another component of aconjugate, such as a targeting moiety (e.g., antibody, ligand,non-covalent protein-binding group, etc.), an analyte, a biomolecule, adrug and the like.

The term “negatively charged substituent”, as used herein, refers to afunctional group present on the nucleic acid reporter compound thatexhibits a negative charge at physiological pH.

The term “nucleic acid” or “nucleic acid polymer” as used herein meansDNA, RNA, single-stranded, double-stranded, or more highly aggregatedhybridization motifs, and any chemical modifications thereof.Modifications include, but are not limited to, those providing chemicalgroups that incorporate additional charge, polarizability, hydrogenbonding, electrostatic interaction, and fluxionality to the nucleic acidligand bases or to the nucleic acid ligand as a whole. Suchmodifications include, but are not limited to, peptide nucleic acids(PNAs), phosphodiester group modifications (e.g., phosphorothioates,methylphosphonates), 2′-position sugar modifications, 5-positionpyrimidine modifications, 8-position purine modifications, modificationsat exocyclic amines, substitution of 4-thiouridine, substitution of5-bromo or 5-iodo-uracil; backbone modifications, methylations, unusualbase-pairing combinations such as the isobases, isocytidine andisoguanidine and the like. Nucleic acids can also include non-naturalbases, such as, for example, nitroindole. Modifications can also include3′ and 5′ modifications such as capping with a quencher, a fluorophoreor another moiety.

The term “nucleic acid reporter molecule” as used herein refers to thepresent cyanine compounds that contain at least one group that isnegatively charged at a physiological pH.

The term “reactive group” as used herein refers to a group that iscapable of reacting with another chemical group to form a covalent bond,i.e. is covalently reactive under suitable reaction conditions, andgenerally represents a point of attachment for another substance. Thereactive group is a moiety, such as carboxylic acid or succinimidylester, on the compounds of the present invention that is capable ofchemically reacting with a functional group on a different compound toform a covalent linkage. Reactive groups generally include nucleophiles,electrophiles and photoactivatable groups.

Exemplary reactive groups include, but are not limited to, olefins,acetylenes, alcohols, phenols, ethers, oxides, halides, aldehydes,ketones, carboxylic acids, esters, amides, cyanates, isocyanates,thiocyanates, isothiocyanates, amines, hydrazines, hydrazones,hydrazides, diazo, diazonium, nitro, nitriles, mercaptans, sulfides,disulfides, sulfoxides, sulfones, sulfonic acids, sulfinic acids,acetals, ketals, anhydrides, sulfates, sulfenic acids isonitriles,amidines, imides, imidates, nitrones, hydroxylamines, oximes, hydroxamicacids thiohydroxamic acids, allenes, ortho esters, sulfites, enamines,ynamines, ureas, pseudoureas, semicarbazides, carbodiimides, carbamates,imines, azides, azo compounds, azoxy compounds, and nitroso compounds.Reactive functional groups also include those used to preparebioconjugates, e.g., N-hydroxysuccinimide esters, maleimides and thelike. Methods to prepare each of these functional groups are well knownin the art and their application to or modification for a particularpurpose is within the ability of one of skill in the art (see, forexample, Sandler and Karo, eds. ORGANIC FUNCTIONAL GROUP PREPARATIONS,Academic Press, San Diego, 1989).

The term “reporter molecule” as used herein refers to any luminescentmolecule that is capable of associating with a nucleic acid polymer andproducing a detectable signal. Typically, reporter molecules includeunsymmetrical cyanine dyes, dimmers of cyanine dyes, ethidium bromide,DAPI, Hoechst, acridine and styryl dyes that are capable of producing adetectable signal upon appropriate wavelength excitation.

The term “salt thereof,” as used herein includes salts of the agents ofthe invention and their conjugates, which are preferably prepared withrelatively nontoxic acids or bases, depending on the particularsubstituents found on the compounds described herein. When compounds ofthe present invention contain relatively acidic functionalities, baseaddition salts can be obtained by contacting the neutral form of suchcompounds with a sufficient amount of the desired base, either neat orin a suitable inert solvent. Examples of base addition salts includesodium, potassium, calcium, ammonium, organic amino, or magnesium, or asimilar salt. When compounds of the present invention contain relativelybasic functionalities, acid addition salts can be obtained by contactingthe neutral form of such compounds with a sufficient amount of thedesired acid, either neat or in a suitable inert solvent. Examples ofaddition salts include those derived from inorganic acids likehydrochloric, hydrobromic, nitric, carbonic, monohydrogencarbonic,phosphoric, monohydrogenphosphoric, dihydrogenphosphoric, sulfuric,monohydrogensulfuric, hydriodic, or phosphorous acids and the like, aswell as the salts derived from relatively nontoxic organic acids likeacetic, propionic, isobutyric, maleic, malonic, benzoic, succinic,suberic, fumaric, lactic, mandelic, phthalic, benzenesulfonic,p-tolylsulfonic, citric, tartaric, methanesulfonic, and the like. Alsoincluded are salts of amino acids such as arginate and the like, andsalts of organic acids like glucuronic or galactunoric acids and thelike (see, for example, Berge et al., “Pharmaceutical Salts”, Journal ofPharmaceutical Science, 1977, 66, 1-19). Certain specific compounds ofthe present invention contain both basic and acidic functionalities thatallow the compounds to be converted into either base or acid additionsalts.

The term “sample” as used herein refers to any material that may containnucleic acid. The sample may also include diluents, buffers, detergents,and contaminating species, debris and the like that are found mixed withthe target. Illustrative examples include urine, sera, blood plasma,total blood, saliva, tear fluid, cerebrospinal fluid, secretory fluidsand the like. Also included are solid, gel or substances such as mucus,body tissues, cells and the like suspended or dissolved in liquidmaterials such as buffers, extractants, solvents and the like.Typically, the sample is a live cell, a biological fluid that comprisesendogenous host cell proteins, nucleic acid polymers, nucleotides,nucleosides, oligonucleotides, peptides and buffer solutions. The samplemay be in an aqueous solution, a viable cell culture or immobilized on asolid or semi solid surface such as a polyacrylamide gel, membrane blotor on a microarray.

The term “solid support,” as used herein, refers to a material that issubstantially insoluble in a selected solvent system, or which can bereadily separated (e.g., by precipitation) from a selected solventsystem in which it is soluble. Solid supports useful in practicing thepresent invention can include groups that are activated or capable ofactivation to allow selected species to be bound to the solid support.Solid supports may be present in a variety of forms, including a chip,wafer or well, onto which an individual, or more than one compound, ofthe invention is bound such as a polymeric bead or particle.

The term “sulfoalkyl,” as used herein refers to a group having thegeneral formula —(CH₂)_(n)SO₃ wherein n is 1-18.

The Compounds

In general, for ease of understanding the present invention, the nucleicacid reporter molecules and corresponding substituents will first bedescribed in detail, followed by the many and varied methods in whichthe compounds find uses, which is followed by exemplified methods of useand synthesis of novel compounds that are particularly advantageous foruse with the methods of the present invention.

The reporter compounds of the present disclosure typically exhibit afluorescence enhancement when non-covalently associated with a nucleicacid. For selected compounds, the fluorescence enhancement is greaterwhen the nucleic acid is DNA than when the nucleic acid is RNA.

In one embodiment the present invention provides nucleic acid complexingcompounds that comprise at least one negatively charged moiety atphysiological pH. Without wishing to be bound by a theory, it appearsthat typically the nucleic acid complexing compounds, when substitutedby a negatively charged moiety, become groove binders instead ofintercalating agents. Thus, negatively charged nucleic acid complexingcompounds, while they appear to associate with both single and doublestranded nucleic acid (RNA and/or DNA) they demonstrate an increasedfluorescent enhancement when associated with double stranded nucleicacid, which is most prevalent as DNA. The nucleic acid complexingcompounds include, without limitation, any compound known to one skilledin the art and novel compounds yet to be discovered, such as cyaninedyes, styryl dyes, ethidium bromide, DAPI, Hoechst and acridine. Thereis no intended limitation on the nucleic acid complexing compound.

A “negatively charged substituent”, as used herein, refers to afunctional group present on the reporter compound that exhibits anegative charge at physiological pH. Although physiological pH is about7.4, it is understood that various organisms and biological componentsmay be evaluated at higher or lower pH values, and that any pH that iscompatible with the organism or biological component of interest may beconsidered a physiological pH. Similarly, any substituent that exhibitsa negative charge at a pH level of interest is an appropriate negativelycharged substituent for the purposes of this disclosure.

Any negatively charged substituent of the reporter compound may conferthe desired nucleic acid selectivity on the reporter compound. Inparticular, preferred negatively charged substituents include, forexample, sulfo, carboxy, phosphate, phosphonate, and hydroxy. Thenegatively charged substituent may be bound directly to the reportercompound, or may be bound via another substituent of the reportercompound. For example, the negatively charged substituent may be boundto the reporter compound via an alkyl group. Typically, the negativelycharged substituent is a sulfo, carboxy, sulfoalkyl, or carboxyalkylsubstituent.

Typically, the nucleic acid complexing compounds are unsymmetricalcyanine dyes including, but are not limited to, any compound disclosedin U.S. Pat. Nos. 4,957,870; 4,883,867; 5,436,134; 5,658,751, 5,534,416and 5,863,753, when substituted with a negatively charged moiety.

1. Cyanine Nucleic Acid Reporter Molecules

In one embodiment, the cyanine dye reporter compounds of the presentdisclosure may be described by the formula:

with the proviso that the compound is substituted by at least onenegatively charged moiety at a physiological pH.

W represents the atoms necessary to form one to two fused 5- or6-membered aromatic rings. The aromatic ring system represented by W isoptionally substituted by any appropriate aryl group substituent, asdescribed above, including reactive functional groups, solid supports,carrier molecules or covalent linkages.

Typically, the W ring system incorporates moieties selected from thegroup consisting of —C, —CR¹, and —N(R²). Each of α and β is 0 or 1.Typically where β is 0, α is 1, and vice versa, so that α+β=1.

In one embodiment, W may incorporates four —CR¹ moieties to form abenzazolium ring system having the formula

The R¹ substituents may include any aryl group substituent, includingadditional fused 5- or 6-membered rings. Where each R¹ is independentlyhydrogen, carboxy, sulfo, phosphate, phosphonate, amino, hydroxyl,trifluoromethyl, halogen, alkyl, substituted alkyl, alkoxy, alkylamino,substituted alkylamino, dialkylamino, substituted dialkylamino, fusedbenzene, substituted fused benzene, trifluomethyl, halogen, reactivegroup, solid support or carrier molecule, wherein each alkyl portion ofwhich is optionally substituted by alkyl group substituents, asdescribed above. In particular, the alkyl groups substituents may beselected from the group consisting of carboxy, sulfo, phosphate,phosphonate, amino, and hydroxy. t is an integer from 1 to 4.

The R² substituent may include any aryl group substituent. R² mayparticularly be a substituted alkyl, unsubstituted alkyl, substitutedarylalkyl, unsubstituted arylalkyl, substituted heteroalkyl,unsubstituted heteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy,hydroxyalkyl, sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino,dialkylamino, or trialkylammonium. The alkyl portion of which optionallyincorporates up to six hetero atoms, selected from the group consistingof N, O and S; and which is optionally substituted one or more times bysubstituents selected from the group consisting of F, Cl, Br, I,hydroxy, carboxy, sulfo, phosphate, amino, sulfate, phosphonate, cyano,nitro, azido, C₁-C₆ alkoxy, C₁-C₆ alkylamino, C₂-C₁₂ dialkylamino, andC₃-C₁₈ trialkylammonium.

The value of n may be 0 or 1. Where n is 0, the reporter compound is amonomethine dye. Where n is 1, the reporter compound is a trimethinedye. Typically, n is 0.

The X moiety is selected from S, O, or Se, forming a benzothiazole,benzoxazole, or benzoselenazole heterocyclic ring system, respectively.Typically, X is S or O, and more typically, X is S.

The D moiety is a substituted or unsubstituted ring system, includingpyridinium and quinolinium ring systems. For example, the D moiety mayinclude the following ring systems (additional substituents omitted forclarity):

The D ring system is optionally further substituted by any aryl groupsubstituent, as described above.

Typically, D will include a pyridinium or quinolinium ring systemaccording to the formula

or the formula

where R³-R⁶ may be selected from among aryl group substituents, or R⁵and R⁶ taken in combination form a fused 6-membered aromatic ring tocomplete a quinolinium ring system. Alternatively a member selected fromR⁵ in combination with R⁶; R⁴ in combination with R⁵; R⁴ in combinationwith R³; R⁴ in combination with R⁶; and R³ in combination with R⁶together with the atoms to which they are joined, form a ring which is a5-, 6- or 7-membered heterocycloalkyl, a substituted 5-, 6- or7-membered heterocycloalkyl, a 5-, 6- or 7-membered cycloalkyl, asubstituted 5-, 6- or 7-membered cycloalkyl, a 5-, 6- or 7-memberedheteroaryl, a substituted 5-, 6- or 7-membered heteroaryl, a 5-, 6- or7-membered aryl or a substituted 5-, 6- or 7-membered aryl.

More particularly, each of R³-R⁶ may be hydrogen, substituted alkyl,unsubstituted alkyl, substituted heteroalkyl, unsubstituted heteroalkyl,substituted aryl, unsubstituted aryl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroarylalkyl; unsubstitutedheteroarylalkyl, substituted heteroaryl, unsubstituted heteroaryl,substituted cycloalkyl, unsubstituted cycloalkyl, substitutedheterocycloalkyl, unsubstituted heterocycloalkyl, halogen, alkoxy,substituted alkylamino, unsubstituted alkylamino, substituted alkylthio,unsubstituted alkylthio, reactive group, solid support, or carriermolecule. Where R⁵ and R⁶ complete a quinolinium ring system, theadditional ring substituents may also be H, alkyl, heteroalkyl, aryl,arylalkyl, heteroarylalkyl; heteroaryl, cycloalkyl, heterocycloalkyl,halogen, alkoxy, alkylamino, alkylthio, or a reactive group.

Selected reporter compounds may include compounds where at least one ofR³ and R⁴ is selected from the group consisting of alkyl, heteroalkyl,alkoxy, alkylthio, aryl, arylalkyl, heteroaryl, and heteroarylalkyl thatis itself then optionally further substituted. More particularly, eachof R³ and R⁴ may be selected from the group consisting of alkyl, phenyl,benzyl, alkylthio, indolyl, imidazolyl, and thiazolyl that is thenoptionally further substituted one or more times. In a particularexample, each of R³ and R⁴ may be selected from the group consisting ofH, alkyl, —(CH₂)_(a)-aryl, and —(CH₂)_(a)-heteroaryl, where a is 0-6 andthe alkyl, aryl, and heteroaryl portions are optionally furthersubstituted one or more times by alkyl or aryl group substituents,respectively.

In an exemplary embodiment, the present compounds have the formula

-   -   or the formula

Wherein each R^(1a) and R^(1b) are independently hydrogen, carboxy,sulfo, phosphate, phosphonate, amino, hydroxyl, trifluoromethyl,halogen, alkyl, substituted alkyl, alkoxy, alkylamino, substitutedalkylamino, dialkylamino, substituted dialkylamino, fused benzene,substituted fused benzene, trifluomethyl, halogen, reactive group, solidsupport or carrier molecule and t is integer from 1 to 4

R² is a substituted alkyl, unsubstituted alkyl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroalkyl, unsubstitutedheteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy, hydroxyalkyl,sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino, dialkylamino, ortrialkylammonium.

R³ and R⁴ are independently hydrogen, substituted alkyl, unsubstitutedalkyl, substituted heteroalkyl, unsubstituted heteroalkyl, substitutedaryl, unsubstituted aryl, substituted arylalkyl, unsubstitutedarylalkyl, substituted heteroarylalkyl; unsubstituted heteroarylalkyl,substituted heteroaryl, unsubstituted heteroaryl, substitutedcycloalkyl, unsubstituted cycloalkyl, substituted heterocycloalkyl,unsubstituted heterocycloalkyl, halogen, alkoxy, substituted alkylamino,unsubstituted alkylamino, substituted alkylthio, unsubstitutedalkylthio, reactive group, solid support, or carrier molecule.

In a further aspect, R⁴ is hydrogen, alkyl, —(CH₂)_(a)-aryl, or—(CH₂)_(a)-heteroaryl, wherein a is an integer from 0 to about 6. In yetanother aspect, R⁴ is an alkyl, phenyl, benzyl, alkylthio, indolyl,imidazolyl, or thiazolyl.

Although the negatively charged substituent may be present at anyposition of the reporter molecule, in one aspect of the invention atleast one of R¹ or R² comprises a negatively charged substituent,typically a sulfo, carboxy, phosphate, or phosphonate, or alkylsubstituted by sulfo, carboxy, phosphate, or phosphonate.

Thus, in an exemplary embodiment, R¹ and R² of Formula IX or X,comprises a negatively charged substituent. Typically at least one of R¹and R² is sulfo, carboxy, phosphate, phosphonate, an alkyl groupsubstituted by sulfo, an alkyl group substituted by a carboxy, an alkylgroup substituted by phosphate, or an alkyl group substituted byphosphonate. Typically, the negatively charged substituent is a sulfo,carboxy, sulfoalkyl, or carboxyalkyl substituent.

Without wishing to be bound by theory, it is believed that the presenceof one or more negatively charged substituents on the cyanine reportercompound may permit the tuning of selectivity and affinity of theresulting compound for particular nucleic acids. In particular, thepresence of at least one negatively charged substituent may increase theselectivity and affinity of the resulting compound for DNA, whencompared to the same compound when binding to RNA. The fluorescenceenhancement of the resulting DNA complex may be greater than that of thecorresponding RNA complex (see Example 31, Table 5).

Alternatively, the presence of at least one negatively chargedsubstituent may increase the selectivity and affinity of the resultingcompound for RNA, when compared to the same compound when binding toDNA. The fluorescence enhancement of the resulting RNA complex may begreater than that of the corresponding DNA complex (see Example 31,Table 6).

The selectivity of a given reporter compound for a particular nucleicacid type may be evaluated using screening methods for observing andquantifying such selectivity, such as are described in Examples 31-37.

The effect of particular negatively charged substituents, orsubstitution at particular positions, may be observed by comparingselected reporter compounds having a negatively charged substituent tocorresponding compounds that do not have the negatively chargedsubstituent. For example, as shown in Table 4, comparison of Compound 27and Compound 30 shows that the addition of a sulfo group as an R¹substituent may create a more than four-fold enhancement of fluorescenceon DNA with respect to RNA. Similarly, a comparison of Compound 25 toCompound 29 shows that the addition of the same R¹ sulfo substituentcreates a 26-fold enhancement of fluorescence on DNA with respect toRNA.

Selected compounds exhibiting selectivity for either DNA or RNA, as wellas screening methods for identifying such selectivity, are described inExamples 1-36.

The compounds disclosed herein are readily modified to permit selectablealteration of the permeability, affinity, absorption, and emissionproperties (for specific examples, see U.S. Pat. No. 5,658,751, herebyincorporated by reference). The resulting compounds may be tailored tocover most of the visible and near-infrared spectrum.

Synthesis

The reporter compounds disclosed herein may be prepared by the treatmentof an appropriately substituted benzazolium precursor with anappropriately substituted pyridinium or quinolinium precursor, and(where n=1) a source for the methine spacer.

Typically each precursor is selected so as to incorporate the desiredand/or appropriate chemical substituents, or functional groups that maybe converted to the desired and/or appropriate chemical substituents.The synthetic strategies and procedures that may be used to prepare andcombine these precursors so as to yield the disclosed compounds isgenerally well understood by one skilled in the art, including a varietyof post-synthetic modifications and variations thereof.

A wide variety of benzazolium derivatives suitable for use as aprecursor compound have been described previously. If X is O, theprecursor compound is a benzoxazolium; if X is S it is abenzothiazolium; and if X is Se it is a benzoselenazolium. Thecommercial availability of suitable starting materials and relative easeof synthesis may make compounds with X═O or S the preferred precursors.

The desired R¹ substituents are typically incorporated in the parentbenzazole molecule prior to quaternization with an alkylating agent. R²is typically obtained by alkylation of the parent heterocycle with analkylating agent. The alkylating reagent may be an alkyl halide such asethyl iodide, an alkylsulfonate such as methyl p-toluenesulfonate or acyclic sulfonate such as propanesultone or butanesultone.

In the synthesis of the reporter compounds, the second heterocyclicprecursor is usually a pyridinium or quinolinium salt that is alreadyappropriately substituted. Alternatively, substituents can beincorporated into the heterocyclic ring structure subsequent toattachment of the benzazolium portion of the dye.

The pyridine and quinoline precursors may be bound adjacent to the ringnitrogen (as for 2-pyridines and 2-quinolines) or may be bound at apoint of attachment para to the ring nitrogen atom (as for 4-pyridinesand 4-quinolines).

When n=0, the synthesis of monomethine dyes commonly utilizes precursorshaving a methyl substituent on one precursor, and a reactive “leavinggroup” that is typically methylthio or chloro, on the other substituent.Typically, the precursors include a methylthio and methyl substituent,respectively. The condensing reagent in the case of monomethine dyes istypically a base such as triethylamine or diisopropylethylamine.

Specific examples of benzazolium, pyridinium, and quinoliniumintermediates that may be useful in completing the synthesis describedabove may be found in, for example, U.S. Pat. Nos. 5,436,134 and5,658,751, each hereby incorporated by reference. Each pyridinium,quinolinium or benzazolium ring system may be fused to additional rings,resulting in dyes that absorb and emit at longer wavelengths (forexample, see U.S. Pat. No. 6,027,709, hereby incorporated by reference).

Examples 1-30 describe the synthesis of selected reporter compounds. Itwill be appreciated that numerous changes and modifications in thedescribed synthetic schemes may be adopted in order to prepare aparticular desired reporter compound, without deviating from the generalsynthetic strategies described herein.

Reactive Groups, Carrier Molecules and Solid Supports

The present compounds, in certain embodiments, are chemically reactivewherein the compounds comprise a reactive group. In a furtherembodiment, the compounds comprise a carrier molecule or solid support.These substituents, reactive groups, carrier molecules, and solidsupports, comprise a linker that is used to covalently attach thesubstituents to any of the moieties of the present compounds. The solidsupport, carrier molecule or reactive group may be directly attached(where linker is a single bond) to the moieties or attached through aseries of stable bonds, as disclosed above.

Any combination of linkers may be used to attach the carrier molecule,solid support or reactive group and the present compounds together. Thelinker may also be substituted to alter the physical properties of thereporter moiety or chelating moiety, such as spectral properties of thedye. Examples of L include substituted or unsubstituted polyalkylene,arylene, alkylarylene, arylenealkyl, or arylthio moieties.

The linker typically incorporates 1-30 nonhydrogen atoms selected fromthe group consisting of C, N, O, S and P. The linker may be anycombination of stable chemical bonds, optionally including, single,double, triple or aromatic carbon-carbon bonds, as well ascarbon-nitrogen bonds, nitrogen-nitrogen bonds, carbon-oxygen bonds,sulfur-sulfur bonds, carbon-sulfur bonds, phosphorus-oxygen bonds,phosphorus-nitrogen bonds, and nitrogen-platinum bonds. Typically thelinker incorporates less than 15 nonhydrogen atoms and are composed ofany combination of ether, thioether, thiourea, amine, ester,carboxamide, sulfonamide, hydrazide bonds and aromatic or heteroaromaticbonds. Typically the linker is a combination of single carbon-carbonbonds and carboxamide, sulfonamide or thioether bonds. The bonds of thelinker typically result in the following moieties that can be found inthe linker: ether, thioether, carboxamide, thiourea, sulfonamide, urea,urethane, hydrazine, alkyl, aryl, heteroaryl, alkoxy, cycloalkyl andamine moieties. Examples of a linker include substituted orunsubstituted polymethylene, arylene, alkylarylene, arylenealkyl, andarylthio.

In one embodiment, the linker contains 1-6 carbon atoms; in another, thelinker comprises a thioether linkage. Exemplary linking members includea moiety that includes —C(O)NH—, —C(O)O—, —NH—, —S—, —O—, and the like.In another embodiment, the linker is or incorporates theformula—(CH₂)_(d)(CONH(CH₂)_(e))_(z)—or where d is an integer from 0-5,e is an integer from 1-5 and z is 0 or 1. In a further embodiment, thelinker is or incorporates the formula —O—(CH₂)—. In yet anotherembodiment, the linker is or incorporates a phenylene or a2-carboxy-substituted phenylene.

An important feature of the linker is to provide an adequate spacebetween the carrier molecule, reactive group or solid support and thedye so as to prevent steric hinderance. Therefore, the linker of thepresent compound is important for (1) attaching the carrier molecule,reactive group or solid support to the compound, (2) providing anadequate space between the carrier molecule, reactive group or solidsupport and the compound so as not to sterically hinder the action ofthe compound and (3) for altering the physical properties of the presentcompounds.

In another exemplary embodiment of the invention, the present compoundsare chemically reactive, and are substituted by at least one reactivegroup. The reactive group functions as the site of attachment foranother moiety, such as a carrier molecule or a solid support, whereinthe reactive group chemically reacts with an appropriate reactive orfunctional group on the carrier molecule or solid support.

Reactive groups or reactive group precursors may be positioned duringthe formation of the present compounds. Thus, compounds incorporating areactive group can be reacted with and attached to a wide variety ofbiomolecules or non-biomolecules that contain or are modified to containfunctional groups with suitable reactivity. When a labeled componentincludes a compound as disclosed herein, then this conjugate typicallypossesses the nucleic acid staining abilities of the parent compound,particularly DNA staining. However, the present fluorescent compoundscan also function as reporter molecules for the labeled componentswherein the nucleic acid binding properties of the reagents may notemployed.

Preferred reactive groups for incorporation into the disclosed compoundsmay be selected to react with an amine, a thiol or an alcohol. In anexemplary embodiment, the compounds of the invention further comprise areactive group that is an acrylamide, an activated ester of a carboxylicacid, a carboxylic ester, an acyl azide, an acyl nitrile, an aldehyde,an alkyl halide, an anhydride, an aniline, an amine, an aryl halide, anazide, an aziridine, a boronate, a diazoalkane, a haloacetamide, ahaloalkyl, a halotriazine, a hydrazine, an imido ester, an isocyanate,an isothiocyanate, a maleimide, a phosphoramidite, a photoactivatablegroup, a reactive platinum complex, a silyl halide, a sulfonyl halide,and a thiol. In a particular embodiment the reactive group is selectedfrom the group consisting of carboxylic acid, succinimidyl ester of acarboxylic acid, hydrazide, amine and a maleimide. In exemplaryembodiment, at least one member selected from R¹, R^(1a), R^(1b), R²,R³, R⁴, R⁵, or R⁶ comprises a reactive group. Preferably, at least oneof R¹, R^(1a), R^(1b), or R² comprises a reactive group or is attachedto a reactive group. Alternatively, if the present compound comprises acarrier molecule or solid support a reactive group may be covalentlyattached independently to those substituents, allowing for furtherconjugation to a another dye, carrier molecule or solid support.

In one aspect, the compound comprises at least one reactive group thatselectively reacts with an amine group. This amine-reactive group isselected from the group consisting of succinimidyl ester, sulfonylhalide, tetrafluorophenyl ester and iosothiocyanates. Thus, in oneaspect, the present compounds form a covalent bond with anamine-containing molecule in a sample. In another aspect, the compoundcomprises at least one reactive group that selectively reacts with athiol group. This thiol-reactive group is selected from the groupconsisting of maleimide, haloalkyl and haloacetamide (including anyreactive groups disclosed in U.S. Pat. Nos. 5,362,628; 5,352,803 and5,573,904).

The pro-reactive groups are synthesized during the formation of themonomer moieties and carrier molecule and solid support containingcompounds to provide chemically reactive compounds. In this way,compounds incorporating a reactive group can be covalently attached to awide variety of carrier molecules or solid supports that contain or aremodified to contain functional groups with suitable reactivity,resulting in chemical attachment of the components. In an exemplaryembodiment, the reactive group of the compounds of the invention and thefunctional group of the carrier molecule or solid support compriseelectrophiles and nucleophiles that can generate a covalent linkagebetween them. Alternatively, the reactive group comprises aphotoactivatable group, which becomes chemically reactive only afterillumination with light of an appropriate wavelength. Typically, theconjugation reaction between the reactive group and the carrier moleculeor solid support results in one or more atoms of the reactive groupbeing incorporated into a new linkage attaching the present compound ofthe invention to the carrier molecule or solid support. Selectedexamples of functional groups and linkages are shown in Table 1, wherethe reaction of an electrophilic group and a nucleophilic group yields acovalent linkage.

TABLE 1 Examples of some routes to useful covalent linkagesElectrophilic Group Nucleophilic Group Resulting Covalent Linkageactivated esters* amines/anilines carboxamides acrylamides thiolsthioethers acyl azides** amines/anilines carboxamides acyl halidesamines/anilines carboxamides acyl halides alcohols/phenols esters acylnitriles alcohols/phenols esters acyl nitriles amines/anilinescarboxamides aldehydes amines/anilines imines aldehydes or ketoneshydrazines hydrazones aldehydes or ketones hydroxylamines oximes alkylhalides amines/anilines alkyl amines alkyl halides carboxylic acidsesters alkyl halides thiols thioethers alkyl halides alcohols/phenolsethers alkyl sulfonates thiols thioethers alkyl sulfonates carboxylicacids esters alkyl sulfonates alcohols/phenols ethers anhydridesalcohols/phenols esters anhydrides amines/anilines carboxamides arylhalides thiols thiophenols aryl halides amines aryl amines aziridinesthiols thioethers boronates glycols boronate esters carbodiimidescarboxylic acids N-acylureas or anhydrides diazoalkanes carboxylic acidsesters epoxides thiols thioethers haloacetamides thiols thioethershaloplatinate amino platinum complex haloplatinate heterocycle platinumcomplex haloplatinate thiol platinum complex halotriazinesamines/anilines aminotriazines halotriazines alcohols/phenols triazinylethers halotriazines thiols triazinyl thioethers imido estersamines/anilines amidines isocyanates amines/anilines ureas isocyanatesalcohols/phenols urethanes isothiocyanates amines/anilines thioureasmaleimides thiols thioethers phosphoramidites alcohols phosphite esterssilyl halides alcohols silyl ethers sulfonate esters amines/anilinesalkyl amines sulfonate esters thiols thioethers sulfonate esterscarboxylic acids esters sulfonate esters alcohols ethers sulfonylhalides amines/anilines sulfonamides sulfonyl halides phenols/alcoholssulfonate esters *Activated esters, as understood in the art, generallyhave the formula —COΩ, where Ω is a good leaving group (e.g.,succinimidyloxy (—OC₄H₄O₂) sulfosuccinimidyloxy (—OC₄H₃O₂—SO₃H),-1-oxybenzotriazolyl (—OC₆H₄N₃); or an aryloxy group or aryloxysubstituted one or more times by electron withdrawing substituents suchas nitro, fluoro, chloro, cyano, or trifluoromethyl, or combinationsthereof, used to form activated aryl esters; or a carboxylic acidactivated by a carbodiimide to form an anhydride or mixed anhydride—OCOR^(a) or —OCNR^(a)NHR^(b), where R^(a) and R^(b), which may be thesame or different, are C₁-C₆ alkyl, C₁-C₆ perfluoroalkyl, or C₁-C₆alkoxy; or cyclohexyl, 3-dimethylaminopropyl, or N-morpholinoethyl).**Acyl azides can also rearrange to isocyanates

Choice of the reactive group used to attach the compound of theinvention to the substance to be conjugated typically depends on thereactive or functional group on the substance to be conjugated and thetype or length of covalent linkage desired. The types of functionalgroups typically present on the organic or inorganic substances(biomolecule or non-biomolecule) include, but are not limited to,amines, amides, thiols, alcohols, phenols, aldehydes, ketones,phosphates, imidazoles, hydrazines, hydroxylamines, disubstitutedamines, halides, epoxides, silyl halides, carboxylate esters, sulfonateesters, purines, pyrimidines, carboxylic acids, olefinic bonds, or acombination of these groups. A single type of reactive site may beavailable on the substance (typical for polysaccharides or silica), or avariety of sites may occur (e.g., amines, thiols, alcohols, phenols), asis typical for proteins.

Typically, the reactive group will react with an amine, a thiol, analcohol, an aldehyde, a ketone, or with silica. Preferably, reactivegroups react with an amine or a thiol functional group, or with silica.In one embodiment, the reactive group is an acrylamide, an activatedester of a carboxylic acid, an acyl azide, an acyl nitrile, an aldehyde,an alkyl halide, a silyl halide, an anhydride, an aniline, an arylhalide, an azide, an aziridine, a boronate, a diazoalkane, ahaloacetamide, a halotriazine, a hydrazine (including hydrazides), animido ester, an isocyanate, an isothiocyanate, a maleimide, aphosphoramidite, a reactive platinum complex, a sulfonyl halide, or athiol group. By “reactive platinum complex” is particularly meantchemically reactive platinum complexes such as described in U.S. Pat.No. 5,714,327.

Where the reactive group is an activated ester of a carboxylic acid,such as a succinimidyl ester of a carboxylic acid, a sulfonyl halide, atetrafluorophenyl ester or an isothiocyanates, the resulting compound isparticularly useful for preparing conjugates of carrier molecules suchas proteins, nucleotides, oligonucleotides, or haptens. Where thereactive group is a maleimide, haloalkyl or haloacetamide (including anyreactive groups disclosed in U.S. Pat. Nos. 5,362,628; 5,352,803 and5,573,904 (supra)) the resulting compound is particularly useful forconjugation to thiol-containing substances. Where the reactive group isa hydrazide, the resulting compound is particularly useful forconjugation to periodate-oxidized carbohydrates and glycoproteins, andin addition is an aldehyde-fixable polar tracer for cell microinjection.Where the reactive group is a silyl halide, the resulting compound isparticularly useful for conjugation to silica surfaces, particularlywhere the silica surface is incorporated into a fiber optic probesubsequently used for remote ion detection or quantitation.

In a particular aspect, the reactive group is a photoactivatable groupsuch that the group is only converted to a reactive species afterillumination with an appropriate wavelength. An appropriate wavelengthis generally a UV wavelength that is less than 400 nm. This methodprovides for specific attachment to only the target molecules, either insolution or immobilized on a solid or semi-solid matrix.Photoactivatable reactive groups include, without limitation,benzophenones, aryl azides and diazirines.

Preferably, the reactive group is a photoactivatable group, succinimidylester of a carboxylic acid, a haloacetamide, haloalkyl, a hydrazine, anisothiocyanate, a maleimide group, an aliphatic amine, a silyl halide, acadaverine or a psoralen. More preferably, the reactive group is asuccinimidyl ester of a carboxylic acid, a maleimide, an iodoacetamide,or a silyl halide. In a particular embodiment the reactive group is asuccinimidyl ester of a carboxylic acid, a sulfonyl halide, atetrafluorophenyl ester, an iosothiocyanates or a maleimide.

The selection of a covalent linkage to attach the reporter molecule tothe carrier molecule or solid support typically depends on thechemically reactive group on the component to be conjugated. Thediscussion regarding reactive groups in the section immediatelypreceding is relevant here as well. Exemplary reactive groups typicallypresent on the biological or non-biological components include, but arenot limited to, amines, thiols, alcohols, phenols, aldehydes, ketones,phosphates, imidazoles, hydrazines, hydroxylamines, disubstitutedamines, halides, epoxides, sulfonate esters, purines, pyrimidines,carboxylic acids, or a combination of these groups. A single type ofreactive site may be available on the component (typical forpolysaccharides), or a variety of sites may occur (e.g. amines, thiols,alcohols, phenols), as is typical for proteins. A carrier molecule orsolid support may be conjugated to more than one reporter molecule,which may be the same or different, or to a substance that isadditionally modified by a hapten. Although some selectivity can beobtained by careful control of the reaction conditions, selectivity oflabeling is best obtained by selection of an appropriate reactivecompound.

In another exemplary embodiment, the present compound is covalentlybound to a carrier molecule. If the compound has a reactive group, thenthe carrier molecule can alternatively be linked to the compound throughthe reactive group. The reactive group may contain both a reactivefunctional moiety and a linker, or only the reactive functional moiety.

A variety of carrier molecules are useful in the present invention.Exemplary carrier molecules include antigens, steroids, vitamins, drugs,haptens, metabolites, toxins, environmental pollutants, amino acids,peptides, proteins, nucleic acids, nucleic acid polymers, carbohydrates,lipids, and polymers. In exemplary embodiment, at least one memberselected from R¹, R^(1a), R^(1b), R², R³, R⁴, R⁵, or R⁶ comprises acarrier molecule. Preferably, at least one of R¹, R^(1a), R^(1b), or R²comprises a carrier molecule or is attached to a carrier molecule.Alternatively, if the present compound comprises a reactive group orsolid support a reactive group may be covalently attached independentlyto those substituents, allowing for further conjugation to a reactivegroup, carrier molecule or solid support.

In an exemplary embodiment, the carrier molecule comprises an aminoacid, a peptide, a protein, a polysaccharide, a nucleoside, anucleotide, an oligonucleotide, a nucleic acid, a hapten, a psoralen, adrug, a hormone, a lipid, a lipid assembly, a synthetic polymer, apolymeric microparticle, a biological cell, a virus and combinationsthereof. In another exemplary embodiment, the carrier molecule isselected from a hapten, a nucleotide, an oligonucleotide, a nucleic acidpolymer, a protein, a peptide or a polysaccharide. In a preferredembodiment the carrier molecule is amino acid, a peptide, a protein, apolysaccharide, a nucleoside, a nucleotide, an oligonucleotide, anucleic acid, a hapten, a psoralen, a drug, a hormone, a lipid, a lipidassembly, a tyramine, a synthetic polymer, a polymeric microparticle, abiological cell, cellular components, an ion chelating moiety, anenzymatic substrate or a virus. In another preferred embodiment, thecarrier molecule is an antibody or fragment thereof, an antigen, anavidin or streptavidin, a biotin, a dextran, an antibody bindingprotein, a fluorescent protein, agarose, and a non-biologicalmicroparticle. Typically, the carrier molecule is an antibody, anantibody fragment, antibody-binding proteins, avidin, streptavidin, atoxin, a lectin, or a growth factor. Preferred haptens include biotin,digoxigenin and fluorophores.

Antibody binding proteins include, but are not limited to, protein A,protein G, soluble Fc receptor, protein L, lectins, anti-IgG, anti-IgA,anti-IgM, anti-IgD, anti-IgE or a fragment thereof.

In an exemplary embodiment, the enzymatic substrate is selected from anamino acid, peptide, sugar, alcohol, alkanoic acid, 4-guanidinobenzoicacid, nucleic acid, lipid, sulfate, phosphate, —CH₂OCOalkyl andcombinations thereof. Thus, the enzyme substrates can be cleave byenzymes selected from the group consisting of peptidase, phosphatase,glycosidase, dealkylase, esterase, guanidinobenzotase, sulfatase,lipase, peroxidase, histone deacetylase, endoglycoceramidase,exonuclease, reductase and endonuclease.

In another exemplary embodiment, the carrier molecule is an amino acid(including those that are protected or are substituted by phosphates,carbohydrates, or C₁ to C₂₂ carboxylic acids), or a polymer of aminoacids such as a peptide or protein. In a related embodiment, the carriermolecule contains at least five amino acids, more preferably 5 to 36amino acids. Exemplary peptides include, but are not limited to,neuropeptides, cytokines, toxins, protease substrates, and proteinkinase substrates. Other exemplary peptides may function as organellelocalization peptides, that is, peptides that serve to target theconjugated compound for localization within a particular cellularsubstructure by cellular transport mechanisms. Preferred protein carriermolecules include enzymes, antibodies, lectins, glycoproteins, histones,albumins, lipoproteins, avidin, streptavidin, protein A, protein G,phycobiliproteins and other fluorescent proteins, hormones, toxins andgrowth factors. Typically, the protein carrier molecule is an antibody,an antibody fragment, avidin, streptavidin, a toxin, a lectin, or agrowth factor. Exemplary haptens include biotin, digoxigenin andfluorophores.

In another exemplary embodiment, the carrier molecule comprises anucleic acid base, nucleoside, nucleotide or a nucleic acid polymer,optionally containing an additional linker or spacer for attachment of afluorophore or other ligand, such as an alkynyl linkage (U.S. Pat. No.5,047,519), an aminoallyl linkage (U.S. Pat. No. 4,711,955) or otherlinkage. In another exemplary embodiment, the nucleotide carriermolecule is a nucleoside or a deoxynucleoside or a dideoxynucleoside.

Exemplary nucleic acid polymer carrier molecules are single- ormulti-stranded, natural or synthetic DNA or RNA oligonucleotides, orDNA/RNA hybrids, or incorporating an unusual linker such as morpholinederivatized phosphates (AntiVirals, Inc., Corvallis Oreg.), or peptidenucleic acids such as N-(2-aminoethyl)glycine units, where the nucleicacid contains fewer than 50 nucleotides, more typically fewer than 25nucleotides.

In another exemplary embodiment, the carrier molecule comprises acarbohydrate or polyol that is typically a polysaccharide, such asdextran, FICOLL, heparin, glycogen, amylopectin, mannan, inulin, starch,agarose and cellulose, or is a polymer such as a poly(ethylene glycol).In a related embodiment, the polysaccharide carrier molecule includesdextran, agarose or FICOLL.

In another exemplary embodiment, the carrier molecule comprises a lipid(typically having 6-25 carbons), including glycolipids, phospholipids,and sphingolipids. Alternatively, the carrier molecule comprises a lipidvesicle, such as a liposome, or is a lipoprotein (see below). Somelipophilic substituents are useful for facilitating transport of theconjugated dye into cells or cellular organelles.

Alternatively, the carrier molecule is cells, cellular systems, cellularfragments, or subcellular particles. Examples of this type of conjugatedmaterial include virus particles, bacterial particles, virus components,biological cells (such as animal cells, plant cells, bacteria, oryeast), or cellular components. Examples of cellular components that canbe labeled, or whose constituent molecules can be labeled, include butare not limited to lysosomes, endosomes, cytoplasm, nuclei, histones,mitochondria, Golgi apparatus, endoplasmic reticulum and vacuoles.

In another embodiment the carrier molecule is a metal chelating moiety.While any chelator that binds a metal ion of interest and gives a changein its fluorescence properties is a suitable conjugate, preferred metalchelating moieties are crown ethers, including diaryldiaza crown ethers,as described in U.S. Pat. No. 5,405,975 to Kuhn et al. (1995);derivatives of 1,2-bis-(2-aminophenoxyethane)-N,N,N′,N′-tetraacetic acid(BAPTA), as described in U.S. Pat. No. 5,453,517 to Kuhn et al. (1995)(incorporated by reference) and U.S. Pat. No. 5,049,673 to Tsien et al.(1991); derivatives of 2-carboxymethoxy-aniline-N,N-diacetic acid(APTRA), as described by Ragu et al., Am. J. Physiol., 256: C540 (1989);and pyridyl-based and phenanthroline metal ion chelators, as describedin U.S. Pat. No. 5,648,270 to Kuhn et al. (1997).

Fluorescent conjugates of metal chelating moieties possess utility asindicators for the presence of a desired metal ion. While fluorescention-indicators are known in the art, the incorporation of thefluorinated fluorogenic and fluorescent compounds of the presentinvention imparts the highly advantageous properties of the instantfluorophores onto the resulting ion indicator.

The ion-sensing conjugates of the invention are optionally prepared inchemically reactive forms and further conjugated to polymers such asdextrans to improve their utility as sensors as described in U.S. Pat.Nos. 5,405,975 and 5,453,517.

In another exemplary embodiment, the carrier molecule non-covalentlyassociates with organic or inorganic materials. Exemplary embodiments ofthe carrier molecule that possess a lipophilic substituent can be usedto target lipid assemblies such as biological membranes or liposomes bynon-covalent incorporation of the dye compound within the membrane,e.g., for use as probes for membrane structure or for incorporation inliposomes, lipoproteins, films, plastics, lipophilic microspheres orsimilar materials.

In an exemplary embodiment, the carrier molecule comprises a specificbinding pair member wherein the present compounds are conjugated to aspecific binding pair member and are used to detect an analyte in asample. Alternatively, the presence of the labeled specific binding pairmember indicates the location of the complementary member of thatspecific binding pair; each specific binding pair member having an areaon the surface or in a cavity which specifically binds to, and iscomplementary with, a particular spatial and polar organization of theother. Exemplary binding pairs are set forth in Table 2.

TABLE 2 Representative Specific Binding Pairs antigen antibody biotinavidin (or streptavidin or anti-biotin) IgG* protein A or protein G drugdrug receptor folate folate binding protein toxin toxin receptorcarbohydrate lectin or carbohydrate receptor peptide peptide receptorprotein protein receptor enzyme substrate enzyme DNA (RNA) cDNA (cRNA)†hormone hormone receptor ion chelator antibody antibody-binding proteins*IgG is an immunoglobulin †cDNA and cRNA are the complementary strandsused for hybridization

In an exemplary embodiment, the present compounds of the invention arecovalently bonded to a solid support. The solid support may be attachedto the compound or through a reactive group, if present, or through acarrier molecule, if present. In exemplary embodiment, at least onemember selected from R¹, R^(1a), R^(1b), R², R³, R⁴, R⁵, or R⁶ comprisesa solid support. Preferably, at least one of R¹, R^(1a), R^(1b), or R²comprises a solid support or is attached to a solid support.Alternatively, if the present compound comprises a carrier molecule orreactive group a solid support may be covalently attached independentlyto those substituents, allowing for further conjugation to a anotherdye, carrier molecule or solid support.

A solid support suitable for use in the present invention is typicallysubstantially insoluble in liquid phases. Solid supports of the currentinvention are not limited to a specific type of support. Rather, a largenumber of supports are available and are known to one of ordinary skillin the art. Thus, useful solid supports include solid and semi-solidmatrixes, such as aerogels and hydrogels, resins, beads, biochips(including thin film coated biochips), microfluidic chip, a siliconchip, multi-well plates (also referred to as microtitre plates ormicroplates), membranes, conducting and nonconducting metals, glass(including microscope slides) and magnetic supports. More specificexamples of useful solid supports include silica gels, polymericmembranes, particles, derivatized plastic films, glass beads, cotton,plastic beads, alumina gels, polysaccharides such as Sepharose,poly(acrylate), polystyrene, poly(acrylamide), polyol, agarose, agar,cellulose, dextran, starch, FICOLL, heparin, glycogen, amylopectin,mannan, inulin, nitrocellulose, diazocellulose, polyvinylchloride,polypropylene, polyethylene (including poly(ethylene glycol)), nylon,latex bead, magnetic bead, paramagnetic bead, superparamagnetic bead,starch and the like.

In some embodiments, the solid support may include a solid supportreactive functional group, including, but not limited to, hydroxyl,carboxyl, amino, thiol, aldehyde, halogen, nitro, cyano, amido, urea,carbonate, carbamate, isocyanate, sulfone, sulfonate, sulfonamide,sulfoxide, etc., for attaching the compounds of the invention. Usefulreactive groups are disclosed above and are equally applicable to thesolid support reactive functional groups herein.

A suitable solid phase support can be selected on the basis of desiredend use and suitability for various synthetic protocols. For example,where amide bond formation is desirable to attach the compounds of theinvention to the solid support, resins generally useful in peptidesynthesis may be employed, such as polystyrene (e.g., PAM-resin obtainedfrom Bachem Inc., Peninsula Laboratories, etc.), POLYHIPE™ resin(obtained from Aminotech, Canada), polyamide resin (obtained fromPeninsula Laboratories), polystyrene resin grafted with polyethyleneglycol (TentaGel™, Rapp Polymere, Tubingen, Germany),polydimethyl-acrylamide resin (available from Milligen/Biosearch,California), or PEGA beads (obtained from Polymer Laboratories).

Preparation of Conjugates

Conjugates of components (carrier molecules or solid supports), e.g.,drugs, peptides, toxins, nucleotides, phospholipids and other organicmolecules are prepared by organic synthesis methods using the reactivedyes, are generally prepared by means well recognized in the art(Haugland, MOLECULAR PROBES HANDBOOK, supra, 2002). Conjugation to forma covalent bond may consist of simply mixing the reactive dyes of thepresent invention in a suitable solvent in which both the reactivecompound and the substance to be conjugated are soluble. The reactionpreferably proceeds spontaneously without added reagents at roomtemperature or below. For those reactive dyes that are photoactivated,conjugation is facilitated by illumination of the reaction mixture toactivate the reactive dye. Chemical modification of water-insolublesubstances, so that a desired dye-conjugate may be prepared, ispreferably performed in an aprotic solvent such as dimethylformamide(DMF), dimethylsulfoxide (DMSO), acetone, ethyl acetate, toluene, orchloroform.

Preparation of Peptide or Protein Conjugates Typically Comprises FirstDissolving the Protein to be conjugated in aqueous buffer at about 1-10mg/mL at room temperature or below. Bicarbonate buffers (pH about 8.3)are especially suitable for reaction with succinimidyl esters, phosphatebuffers (pH about 7.2-8) for reaction with thiol-reactive functionalgroups and carbonate or borate buffers (pH about 9) for reaction withisothiocyanates and dichlorotriazines. The appropriate reactive dye isthen dissolved in a nonhydroxylic solvent (usually DMSO or DMF) in anamount sufficient to give a suitable degree of conjugation when added toa solution of the protein to be conjugated. The appropriate amount ofcompound for any protein or other component is convenientlypredetermined by experimentation in which variable amounts of the dyeare added to the protein, the conjugate is chromatographically purifiedto separate unconjugated compound and the compound-protein conjugate istested in its desired application.

Following addition of the reactive compound to the component solution,the mixture may be incubated for a suitable period (typically about 1hour at room temperature to several hours on ice), the excess unreactedcompound is removed by gel filtration, dialysis, HPLC, adsorption on anion exchange or hydrophobic polymer or other suitable means. Theconjugate is used in solution or lyophilized. In this way, suitableconjugates can be prepared from antibodies, antibody fragments, avidins,lectins, enzymes, proteins A and G, cellular proteins, albumins,histones, growth factors, hormones, and other proteins. The approximatedegree of substitution is determined from the long wavelength absorptionof the compound-protein conjugate by using the extinction coefficient ofthe un-reacted compound at its long wavelength absorption peak, theunmodified protein's absorption peak in the ultraviolet and bycorrecting the UV absorption of the conjugate for absorption by thecompound in the UV.

Conjugates of polymers, including biopolymers and other higher molecularweight polymers are typically prepared by means well recognized in theart (for example, Brinkley et al., Bioconjugate Chem., 3: 2 (1992)). Inthese embodiments, a single type of reactive site may be available, asis typical for polysaccharides or multiple types of reactive sites (e.g.amines, thiols, alcohols, phenols) may be available, as is typical forproteins. Selectivity of labeling is best obtained by selection of anappropriate reactive dye. For example, modification of thiols with athiol-selective reagent such as a haloacetamide or maleimide, ormodification of amines with an amine-reactive reagent such as anactivated ester, acyl azide, isothiocyanate or3,5-dichloro-2,4,6-triazine. Partial selectivity can also be obtained bycareful control of the reaction conditions.

When modifying polymers with the compounds, an excess of the compound istypically used, relative to the expected degree of dye substitution. Anyresidual, un-reacted compound or hydrolysis product is typically removedby dialysis, chromatography or precipitation. Presence of residual,unconjugated compound can be detected by thin layer chromatography usinga solvent that elutes the compound away from its conjugate. In all casesit is usually preferred that the reagents be kept as concentrated aspractical so as to obtain adequate rates of conjugation.

In an exemplary embodiment, the conjugate is associated with anadditional substance that binds either to the compound or the labeledcomponent through noncovalent interaction. In another exemplaryembodiment, the additional substance is an antibody, an enzyme, ahapten, a lectin, a receptor, an oligonucleotide, a nucleic acid, aliposome, or a polymer. The additional substance is optionally used toprobe for the location of the conjugate, for example, as a means ofenhancing the signal of the conjugate.

Method of Use

The present nucleic acid reporter molecules may be utilized withoutlimit for the fluorescent detection of nucleic acid polymers in a testsample. The methods for the detection of single, double, triple orquadruple stranded DNA and RNA or a combination thereof comprisescontacting a sample with a present nucleic acid reporter molecule toprepare a labeling mixture, incubating the sample with the stainingsolution for a sufficient amount of time for the present reportermolecules to complex with the nucleic acid, illuminating the sample withan appropriate wavelength and observing the illuminated labeling mixturewhereby the nucleic acid polymer is detected.

The compound is typically combined with the sample as a stainingsolution. The staining solution is typically prepared by dissolving apresent nucleic acid reporter molecule in an aqueous solvent such aswater, a buffer solution or assay solution, such as phosphate bufferedsaline, or an organic solvent such as dimethylsulfoxide (DMSO),dimethylformamide (DMF), methanol, ethanol or acetonitrile. Typically,the present nucleic reporter molecules are first dissolved in an organicsolvent such as DMSO as a stock solution. The stock solution istypically prepared about 300-100× more concentrated that the effectiveworking concentration. Thus, the stock solution is diluted to aneffective working concentration in an aqueous solution that optionallyincludes appropriate buffering components and a detergent. An effectiveworking concentration of the present compounds is the amount sufficientto give a detectable optical response when complexed with nucleic acidpolymers. Typically, the effective amount is about 100 nM to 100 μM.Most preferred is about 600 nM to 10 μM. For selected reportercompounds, staining is optimal when the staining solution has aconcentration of about 2.0 μM (see Example 35). It is generallyunderstood that the specific amount of the nucleic acid reportermolecules present in a staining solution is determined by the physicalnature of the sample and the nature of the analysis being performed.

In an exemplary embodiment, the staining solution contains a detergent.This is particularly useful when the nucleic acid is present in anaqueous sample solution. Without wishing to be bound by a theory itappears that a low concentration of detergent stabilizes the presentnucleic acid reporter molecule when present in solution. Thus thestaining solution can be combined with an aqueous sample providing anoptimized solution based detection assay. Detergents include, but arenot limited to, CHAPS, Triton-X, SDS and Tween 20. The detergent istypically present in an aqueous solution at a concentration from about0.01% to about 0.5% (w/v). More specifically the detergent is presentfrom about 0.1% to about 0.3% (w/v). In an exemplary embodiment astaining solution comprises a present nucleic acid reporter moleculepresent at about 2.0 μM and a the detergent CHAPS present at about 0.2%(w/v)

The sample may be combined with the staining solution by any means thatfacilitates contact between the nucleic acid reporter molecules and thenucleic acid. The contact can occur through simple mixing, as in thecase where the sample is a solution. The present reporter molecules maybe added to the nucleic acid solution directly or may contact thesolution on an inert matrix such as a blot or gel, a testing strip, amicroarray, or any other solid or semi-solid surface, for example whereonly a simple and visible demonstration of the presence of nucleic acidsis desired. Any inert matrix used to separate the sample can be used todetect the presence of nucleic acids by observing the fluorescentresponse on the inert matrix. Thus, in one embodiment is provided acomposition comprising a sample and a present nucleic acid reportermolecule.

Alternatively, the sample may include cells and/or cell membranes. Whileselected examples of the compound disclosed herein may permeate cellularmembranes rapidly and completely upon addition of the staining solution,any technique that is suitable for transporting the reporter moleculesacross cell membranes with minimal disruption of the viability of thecell and integrity of cell membranes is a valid method of combining thesample with the present reporter molecules for detection ofintracellular nucleic acid. Examples of suitable processes includeaction of chemical agents such as detergents, enzymes or adenosinetriphosphate; receptor- or transport protein-mediated uptake;pore-forming proteins; microinjection; electroporation; hypoosmoticshock; or minimal physical disruption such as scrape loading orbombardment with solid particles coated with or in the presence of thepresent reporter molecules.

The sample is incubated in the presence of the nucleic acid reportermolecules for a time sufficient to form the fluorescent nucleicacid-reporter molecule complex. Detectable fluorescence in a solution ofnucleic acids is essentially instantaneous. Detectable fluorescencewithin cell membranes requires the permeation of the dye into the cell.While most present nucleic acid reporter molecules are not cell permeantdue to the presence of at least one negatively charged moiety, it isenvisioned that the present compounds could be adequately substituted toprovide cell permeant versions of the present compounds. In general,visibly detectable fluorescence can be obtained in a wide variety ofcells with certain cell permeant embodiments of the present inventionwithin about 10-30 minutes after combination with the sample, commonlywithin about 10-20 minutes. While permeation and fluorescence should berapid for all reporter molecules comprising an aromatic substituent onthe pyridinium or quinolinium moiety of the D moiety, it is readilyapparent to one skilled in the art that the time necessary forsufficient permeation of the dye, or sufficient formation of thefluorescent nucleic acid complex, is dependent upon the physical andchemical nature of the individual sample and the sample medium.

In another embodiment, is provided a complex comprising a presentnucleic acid reporter molecule and a nucleic acid polymer. To facilitatethe detection of the nucleic acid-reporter molecule complex, theexcitation or emission properties of the fluorescent complex areutilized. For example, the sample is excited by a light source capableof producing light at or near the wavelength of maximum absorption ofthe fluorescent complex, such as an ultraviolet or visible lamp, an arclamp, a laser, or even sunlight. Preferably the fluorescent complex isexcited at a wavelength equal to or greater than about 300 nm, morepreferably equal to or greater than about 340 nm. The fluorescence ofthe complex is detected qualitatively or quantitatively by detection ofthe resultant light emission at a wavelength of greater than about 400nm, more preferably greater than about 450 nm, most preferred greaterthan 480 nm. The emission is detected by means that include visibleinspection, photographic film, or the use of current instrumentationsuch as fluorometers, quantum counters, plate readers, epifluorescencemicroscopes and flow cytometers or by means for amplifying the signalsuch as a photomultiplier.

In an exemplified embodiment, the present nucleic acid reportercompounds are used to detect DNA in the presence of RNA, wherein themethod comprises the following steps:

-   -   a. combining a present nucleic acid reporter molecule with a        sample to prepare a labeling mixture, wherein the nucleic acid        reporter molecule has a DNA/RNA ratio of fluorescence        enhancement greater than about one;    -   b. incubating the labeling mixture for a sufficient amount of        time for the nucleic acid reporter molecule to associate with        DNA in the sample to form an incubated mixture;    -   c. illuminating the incubated mixture with an appropriate        wavelength to form an illuminated mixture; and,    -   d. observing the illuminated mixture whereby the DNA is detected        in the presence of RNA.

Typically, the fluorescence of the DNA complex is distinguishable fromthe fluorescence of a RNA complex with the compound. This difference maybe due to any detectable optical property, but in one embodiment, thefluorescence of the DNA complex is brighter than the fluorescence of acorresponding RNA complex with the compound. Therefore, in an exemplaryembodiment, by comparing the fluorescence response of the DNA complexwith a standard, the amount of DNA in the sample may be quantitated,even in the presence of RNA.

As discussed above, the DNA present in the sample may be present in asolution, or in or on a solid or semisolid support. In a preferredembodiment, the nucleic acid is present in a solution. The detection ofDNA in solution may also be enhanced by the addition of a detergent tothe staining solution. Exemplified detergents include, but are notlimited to CHAPS, Triton-X, SDS and Tween 20. Particularly preferred isCHAPS, wherein the fluorescent single in an aqueous signal is stabilizedfor at least 6 hours.

The method may also be enhanced by the addition of an additionaldetection reagent that exhibits a greater fluorescence response whenassociated with RNA than when associated with DNA. A variety of nucleicacid stains that fluoresce brightly when complexed with RNA are known inthe art.

The present nucleic acid reporter molecules that are capable ofproducing a fluorescent intensity signal that is greater on DNA than onRNA are determined empirically. The relative selectivity of the presentcompounds for differentiating DNA and RNA may be readily evaluated asset out in Examples 31-36.

The foregoing methods having been described it is understood that themany and varied compounds of the present invention can be utilized withthe many methods. The compounds not being limited to just those that arespecifically disclosed.

In an exemplary embodiment the present methods employ a nucleic acidreporter molecule that comprises the formula

wherein the compound comprises at lest one negatively charged moiety ata physiological pH. Negatively charged moieties include, sulfo, carboxy,phosphate, phosphonate, an alkyl group substituted by sulfo, an alkylgroup substituted by a carboxy, an alkyl group substituted by phosphate,or an alkyl group substituted by phosphonate.

These nucleic acid reporter molecules exhibit a fluorescence enhancementwhen non-covalently associated with a nucleic acid molecule. In oneaspect, the fluorescence enhancement is greater when the nucleic acid isDNA than when the nucleic acid is RNA. In another aspect, thefluorescence enhancement is greater when the nucleic acid is RNA thanwhen the nucleic acid is DNA.

W represents the atoms necessary to form one or two fused substituted 5-or 6-membered aromatic rings or one or two unsubstituted 5- or6-membered aromatic rings. In an exemplary embodiment W comprises —C,—CR¹, or —N(R²)_(β); wherein β is 0 or 1, provided that α+β=1.

Each R¹ is independently hydrogen, a reactive group, a carrier molecule,a solid support, carboxy, sulfo, phosphate, phosphonate, amino, hydroxy,substituted aryl, unsubstituted aryl, substituted heteroaryl,unsubstituted heteroaryl, trifluoromethyl, halogen, substituted alkyl,unsubstituted alkyl, alkoxy, substituted alkylamino, unsubstitutedalkylamino, substituted dialkylamino, or unsubstituted dialkylamino. Inone aspect, includes a fused 6-membered aromatic ring.

R² is a substituted alkyl, unsubstituted alkyl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroalkyl, unsubstitutedheteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy, hydroxyalkyl,sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino, dialkylamino, ortrialkylammonium. X is O, S, or Se.

n is 0 or 1. In one aspect, n is 0.

D is a substituted pyridinium, unsubstituted pyridinium, substitutedquinolinium, or unsubstituted quinolinium moiety. In one aspect, D hasthe formula

R³, R⁴, R⁵ and R⁶ are independently hydrogen, substituted alkyl,unsubstituted alkyl, substituted heteroalkyl, unsubstituted heteroalkyl,substituted aryl, unsubstituted aryl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroarylalkyl; unsubstitutedheteroarylalkyl, substituted heteroaryl, unsubstituted heteroaryl,substituted cycloalkyl, unsubstituted cycloalkyl, substitutedheterocycloalkyl, unsubstituted heterocycloalkyl, halogen, alkoxy,substituted alkylamino, unsubstituted alkylamino, substituted alkylthio,unsubstituted alkylthio, reactive group, solid support, or carriermolecule.

In one aspect, the D moiety forms a quinolinium moiety when R⁵ and R⁶,along with the atoms they are joined to, form a 6 membered aromaticring. Alternatively, a member selected from R⁵ in combination with R⁶;R⁴ in combination with R⁵; R⁴ in combination with R³; R⁴ in combinationwith R⁶; and R³ in combination with R⁶; together with the atoms to whichthey are joined, form a ring which is a 5-, 6- or 7-memberedheterocycloalkyl, a substituted 5-, 6- or 7-membered heterocycloalkyl, a5-, 6- or 7-membered cycloalkyl, a substituted 5-, 6- or 7-memberedcycloalkyl, a 5-, 6- or 7-membered heteroaryl, a substituted 5-, 6- or7-membered heteroaryl, a 5-, 6- or 7-membered aryl or a substituted 5-6-or 7-membered aryl.

In one aspect at least one of R³ and R⁴ is alkyl, substituted alkyl,heteroalkyl, substituted heteroalkyl, alkoxy, alkylthio, aryl,substituted aryl, arylalkyl, substituted arylalkyl, heteroaryl,substituted heteroaryl, heteroarylalkyl or substituted heteroarylalkyl.In another aspect, R³ and R⁴ are independently alkyl, substituted alkyl,phenyl, substituted phenyl, benzyl, substituted benzyl, alkylthio,substituted alkylthio, indolyl, imidazolyl, or thiazolyl. In yet anotheraspect, R³ is hydrogen, alkyl, substituted alkyl, —(CH₂)_(a)-aryl or—(CH₂)_(a)-heteroaryl; and, R⁴ is hydrogen, alkyl, substituted alkyl,—(CH₂)_(a)-aryl or —(CH₂)_(a)-heteroaryl; wherein a is an integer from 0to about 6.

In an exemplary embodiment, the nucleic aid reporter molecule of thepresent methods have the formula:

-   -   or the formula

In this instance each R^(1a) and R^(1b) are independently hydrogen,carboxy, sulfo, phosphate, phosphonate, amino, hydroxyl,trifluoromethyl, halogen, alkyl, substituted alkyl, alkoxy, alkylamino,substituted alkylamino, dialkylamino, substituted dialkylamino, fusedbenzene, substituted fused benzene, trifluomethyl, halogen, reactivegroup, solid support or carrier molecule. t is an integer from 0 toabout 4.

In one aspect R⁴ is hydrogen, alkyl, —(CH₂)_(a)-aryl, or—(CH₂)_(a)-heteroaryl, wherein a is an integer from 0 to about 6. In afurther aspect R⁴ is an alkyl, phenyl, benzyl, alkylthio, indolyl,imidazolyl, or thiazolyl. Typically at least one of R¹ and R² comprisesa negatively charged substituent. An exemplified nucleic acid reportermolecule is Compound 25.

In an exemplary embodiment, the nucleic aid reporter molecule of thepresent methods comprise a reactive group, solid support and carriermolecule wherein these substituents independently comprise a linker thatis a single covalent bond, or a covalent linkage that is linear orbranched, cyclic or heterocyclic, saturated or unsaturated, having 1-20nonhydrogen atoms selected from the group consisting of C, N, P, O andS; and are composed of any combination of ether, thioether, amine,ester, carboxamide, sulfonamide, hydrazide bonds and aromatic orheteroaromatic bonds.

In an exemplary embodiment, the reactive group is an acrylamide, anactivated ester of a carboxylic acid, a carboxylic ester, an acyl azide,an acyl nitrile, an aldehyde, an alkyl halide, an anhydride, an aniline,an amine, an aryl halide, an azide, an aziridine, a boronate, adiazoalkane, a haloacetamide, a haloalkyl, a halotriazine, a hydrazine,an imido ester, an isocyanate, an isothiocyanate, a maleimide, aphosphoramidite, a reactive platinum complex, a silyl halide, a sulfonylhalide, a thiol or a photoactivatable group. In a further aspect, thereactive group is carboxylic acid, succinimidyl ester of a carboxylicacid, hydrazide, amine or a maleimide.

In an exemplary embodiment the carrier molecule is an amino acid, apeptide, a protein, a polysaccharide, a nucleoside, a nucleotide, anoligonucleotide, a nucleic acid polymer, a hapten, a psoralen, a drug, ahormone, a lipid, a lipid assembly, a synthetic polymer, a polymericmicroparticle, a biological cell or a virus. In a further aspect, thecarrier molecule is an antibody or fragment thereof, an avidin orstreptavidin, a biotin, a blood component protein, a dextran, an enzyme,an enzyme inhibitor, a hormone, an IgG binding protein, a fluorescentprotein, a growth factor, a lectin, a lipopolysaccharide, amicroorganism, a metal binding protein, a metal chelating moiety, anon-biological microparticle, a peptide toxin, aphosphotidylserine-binding protein, a structural protein, asmall-molecule drug, or a tyramide.

In an exemplary embodiment, the solid support is a microfluidic chip, asilicon chip, a microscope slide, a microplate well, silica gels,polymeric membranes, particles, derivatized plastic films, glass beads,cotton, plastic beads, alumina gels, polysaccharides, polyvinylchloride,polypropylene, polyethylene, nylon, latex bead, magnetic bead,paramagnetic bead, or superparamagnetic bead. In a further aspect, thesolid support is Sepharose, poly(acrylate), polystyrene,poly(acrylamide), polyol, agarose, agar, cellulose, dextran, starch,FICOLL, heparin, glycogen, amylopectin, mannan, inulin, nitrocellulose,diazocellulose or starch.

Sample Preparation

The sample may be prepared using methods well known in the art forisolating nucleic acid for in vitro and solution based assay detectionor well known methods for live cell or fixed cells for intracellularand/or in vivo detection of nucleic acids. The sample includes, withoutlimitation, any biological derived material that is thought to contain anucleic acid polymer. Alternatively, samples also include material thatnucleic acid polymers have been added to such as a PCR reaction mixture,a polymer gel such as agarose or polyacrylamide gels or a microfluidicassay system. In another aspect of the present disclosure, the samplecan also include a buffer solution that contains nucleic acid polymersto determine the present reporter molecules that are ideal underdifferent assay conditions or to determine the present reportermolecules that are preferential DNA reporters or RNA reporters.

The sample can be a biological fluid such as whole blood, plasma, serum,nasal secretions, sputum, saliva, urine, sweat, transdermal exudates,cerebrospinal fluid, or the like. Biological fluids also include tissueand cell culture medium wherein an analyte of interest has been secretedinto the medium. Alternatively, the sample may be whole organs, tissueor cells from the animal. Examples of sources of such samples includemuscle, eye, skin, gonads, lymph nodes, heart, brain, lung, liver,kidney, spleen, thymus, pancreas, solid tumors, macrophages, mammaryglands, mesothelium, and the like. Cells include without limitationprokaryotic cells such as bacteria, yeast, fungi, mycobacteria andmycoplasma, and eukaryotic cells such as nucleated plant and animalcells that include primary cultures and immortalized cell lines.Typically prokaryotic cells include E. coli and S. aureus. Eukaryoticcells include without limitation ovary cells, epithelial cells,circulating immune cells, β cells, hepatocytes, and neurons.

In an exemplary embodiment, the sample comprises biological fluids,buffer solutions, live cells, fixed cells, eukaryotic cells, prokaryoticcells, nucleic acid polymers, nucleosides, nucleotides, a polymeric gelor tissue sections. In a further aspect, the sample comprises nucleicacid polymers in an aqueous buffer.

The nucleic acid may be either natural (biological in origin) orsynthetic (prepared artificially). The nucleic acid may be present asnucleic acid fragments, oligonucleotides, or nucleic acid polymers. Thenucleic acid may be present in a condensed phase, such as a chromosome.The presence of the nucleic acid in the sample may be due to asuccessful or unsuccessful experimental methodology, undesirablecontamination, or a disease state. Nucleic acid may be present in all,or only part, of a sample, and the presence of nucleic acids may be usedto distinguish between individual samples, or to differentiate a portionor region within a single sample.

The nucleic acid may be enclosed in a biological structure, for examplecontained within a viral particle, an organelle, or within a cell. Thenucleic acids enclosed in biological structures may be obtained from awide variety of environments, including cultured cells, organisms ortissues, unfiltered or separated biological fluids such as urine,cerebrospinal fluid, blood, lymph fluids, tissue homogenate, mucous,saliva, stool, or physiological secretions or environmental samples suchas soil, water and air. The nucleic acid may be endogenous or introducedas foreign material, such as by infection or by transfection. Thepresent nucleic acid reporter molecules can also be used for stainingnucleic acids in a cell or cells that is fixed and treated with routinehistochemical or cytochemical procedures.

Alternatively, the nucleic acid is not enclosed within a biologicalstructure, but is present as a sample solution. The sample solution canvary from one of purified nucleic acids to crude mixtures such as cellextracts, biological fluids and environmental samples. In some cases itis desirable to separate the nucleic acids from a mixture ofbiomolecules or fluids in the solution prior to combination with thepresent reporter molecules. Numerous, well known, techniques exist forseparation and purification of nucleic acids from generally crudemixtures with other proteins or other biological molecules. Theseinclude such means as electrophoretic techniques and chromatographictechniques using a variety of supports.

The sample may be incubated in the presence of the nucleic acid reportermolecules for a time sufficient to form a nucleic acid-reporter moleculecomplex. While permeation and complexation may be more or less rapid forthe compounds disclosed herein, largely depending on the nature of thesubstituents present on the compound. It should be apparent to oneskilled in the art that the time necessary for sufficient permeation ofthe dye, or sufficient formation of the resulting nucleic acid complex,is dependent upon the physical and chemical nature of the individualsample and the sample medium (see for example U.S. Pat. No. 5,658,751).

Illumination

The sample containing a nucleic acid-reporter molecule complex may beilluminated with a wavelength of light selected to give a detectableoptical response, and observed with a means for detecting the opticalresponse. By optical response is meant any detectable calorimetric orluminescent property of the complex. Typically, the optical response isrelated to the excitation or emission properties of the complex.

For example, the sample may be excited by a light source capable ofproducing light at or near the wavelength of maximum absorption of thefluorescent complex, such as an ultraviolet or visible lamp, an arclamp, a laser, or even sunlight. The optical response is optionallydetected by visual inspection, or by use of any of the followingdevices: CCD camera, video camera, photographic film, laser-scanningdevices, fluorometers, photodiodes, quantum counters, epifluorescencemicroscopes, scanning microscopes, flow cytometers, fluorescencemicroplate readers, or by means for amplifying the signal such asphotomultiplier tubes. Where the sample is examined using a flowcytometer, examination of the sample optionally includes sortingportions of the sample according to their fluorescence response.

The wavelengths of the excitation and emission bands of the nucleic acidreporter molecules vary with reporter molecule composition to encompassa wide range of illumination and detection bands. This allows theselection of individual reporter molecules for use with a specificexcitation source or detection filter. In particular, present reportermolecules can be selected that possess excellent correspondence of theirexcitation band with the 488 nm band of the commonly used argon laser oremission bands which are coincident with preexisting filters.

The presence, location, and distribution of nucleic acid, particularlyDNA, may be detected using the spectral properties of thecompound-nucleic acid complex. Once the dye-nucleic acid complex isformed, its presence may be detected and used as an indicator of thepresence, location, or type of nucleic acids in the sample, or as abasis for sorting cells, or as a key to characterizing the sample orcells in the sample. Such characterization may be enhanced by the use ofadditional reagents, including fluorescent reagents. The nucleic acidconcentration in a sample can also be quantified by comparison withknown relationships between the fluorescence of the nucleic acid-dyecomplex and concentration of nucleic acids in the sample. In particular,fluorescence intensity may be compared to a standard curve prepared fromsamples containing known nucleic acid concentrations, particularly DNAconcentrations.

Kits

Suitable kits for forming a nucleic acid-reporter molecule complex anddetecting the nucleic acid also form part of the present disclosure.Such kits can be prepared from readily available materials and reagentsand can come in a variety of embodiments. The contents of the kit willdepend on the design of the assay protocol or reagent for detection ormeasurement. All kits will contain instructions, appropriate reagents,and one or more of the presently disclosed nucleic acid reportermolecules. Typically, instructions include a tangible expressiondescribing the reagent concentration or at least one assay methodparameter such as the relative amounts of reagent and sample to be addedtogether, maintenance time periods for reagent/sample admixtures,temperature, buffer conditions and the like to allow the user to carryout any one of the methods or preparations described above. In oneaspect, the kit is formulated to facilitate the high-throughputscreening of multiple samples, such as may be accomplished usingautomated methods.

Thus, a kit for detecting nucleic acid in a sample may comprise acompound as described above. The kit may further include instructionsfor performing one or more of the above disclosed methods, including thedetection and/or quantitation of DNA in the presence of RNA.

The kit may optionally further include one or more of the following;sample preparation reagents, a buffering agent, nucleic acid standards,an aqueous nucleic acid reporter molecule dilution buffer, an organicsolvent or an additional detection reagent, particularly where theadditional detection reagent is an additional distinct nucleic acidreporter molecule. Where the additional nucleic acid reporter is aRNA-selective nucleic acid stain, the kit may be useful for detectingand/or quantitating DNA in the presence of RNA.

In an exemplified embodiment, the dilution buffer (for the nucleic acidreporter molecule) contains a detergent in a final concentration ofabout 0.01% to about 0.5% (w/v). The detergents are as disclosed aboutand include CHAPS, Triton-X, SDS and Tween 20.

In an exemplified embodiment, a present kit comprises a compoundaccording to Formula IX or Formula X, a dilution buffer solution, DNAstandards and instructions for detecting and/or quantitating DNA in thepresence of RNA. In one aspect the nucleic acid compound is present as aconcentrated stock solution, such as 200×.

The foregoing kits having been described it is understood that the manyand varied compounds of the present invention can be utilized with themany kits. The compounds not being limited to just those that arespecifically disclosed.

In an exemplary embodiment the present kits comprise a nucleic acidreporter molecule that comprises the formula

wherein the compound comprises at lest one negatively charged moiety ata physiological pH. Negatively charged moieties include, sulfo, carboxy,phosphate, phosphonate, an alkyl group substituted by sulfo, an alkylgroup substituted by a carboxy, an alkyl group substituted by phosphate,or an alkyl group substituted by phosphonate.

These nucleic acid reporter molecules exhibit a fluorescence enhancementwhen non-covalently associated with a nucleic acid molecule. In oneaspect, the fluorescence enhancement is greater when the nucleic acid isDNA than when the nucleic acid is RNA. In another aspect, thefluorescence enhancement is greater when the nucleic acid is RNA thanwhen the nucleic acid is DNA.

W represents the atoms necessary to form one or two fused substituted 5-or 6-membered aromatic rings or one or two unsubstituted 5- or6-membered aromatic rings. In an exemplary embodiment W comprises —C,—CR¹, or —N(R²)_(β); wherein β is 0 or 1, provided that α+β=1.

Each R¹ is independently hydrogen, a reactive group, a carrier molecule,a solid support, carboxy, sulfo, phosphate, phosphonate, amino, hydroxy,substituted aryl, unsubstituted aryl, substituted heteroaryl,unsubstituted heteroaryl, trifluoromethyl, halogen, substituted alkyl,unsubstituted alkyl, alkoxy, substituted alkylamino, unsubstitutedalkylamino, substituted dialkylamino, or unsubstituted dialkylamino. Inone aspect, includes a fused 6-membered aromatic ring.

R² is a substituted alkyl, unsubstituted alkyl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroalkyl, unsubstitutedheteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy, hydroxyalkyl,sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino, dialkylamino, ortrialkylammonium. X is O, S, or Se.

n is 0 or 1. In one aspect, n is 0.

D is a substituted pyridinium, unsubstituted pyridinium, substitutedquinolinium, or unsubstituted quinolinium moiety. In one aspect, D hasthe formula

R³, R⁴, R⁵ and R⁶ are independently hydrogen, substituted alkyl,unsubstituted alkyl, substituted heteroalkyl, unsubstituted heteroalkyl,substituted aryl, unsubstituted aryl, substituted arylalkyl,unsubstituted arylalkyl, substituted heteroarylalkyl; unsubstitutedheteroarylalkyl, substituted heteroaryl, unsubstituted heteroaryl,substituted cycloalkyl, unsubstituted cycloalkyl, substitutedheterocycloalkyl, unsubstituted heterocycloalkyl, halogen, alkoxy,substituted alkylamino, unsubstituted alkylamino, substituted alkylthio,unsubstituted alkylthio, reactive group, solid support, or carriermolecule.

In one aspect, the D moiety forms a quinolinium moiety when R⁵ and R⁶,along with the atoms they are joined to, form a 6 membered aromaticring. Alternatively, a member selected from R⁵ in combination with R⁶;R⁴ in combination with R⁵; R⁴ in combination with R³; R⁴ in combinationwith R⁶; and R³ in combination with R⁶; together with the atoms to whichthey are joined, form a ring which is a 5-, 6- or 7-memberedheterocycloalkyl, a substituted 5-, 6- or 7-membered heterocycloalkyl, a5-, 6- or 7-membered cycloalkyl, a substituted 5-, 6- or 7-memberedcycloalkyl, a 5-, 6- or 7-membered heteroaryl, a substituted 5-, 6- or7-membered heteroaryl, a 5-, 6- or 7-membered aryl or a substituted 5-,6- or 7-membered aryl.

In one aspect at least one of R³ and R⁴ is alkyl, substituted alkyl,heteroalkyl, substituted heteroalkyl, alkoxy, alkylthio, aryl,substituted aryl, arylalkyl, substituted arylalkyl, heteroaryl,substituted heteroaryl, heteroarylalkyl or substituted heteroarylalkyl.In another aspect, R³ and R⁴ are independently alkyl, substituted alkyl,phenyl, substituted phenyl, benzyl, substituted benzyl, alkylthio,substituted alkylthio, indolyl, imidazolyl, or thiazolyl. In yet anotheraspect, R³ is hydrogen, alkyl, substituted alkyl, —(CH₂)_(a)-aryl or—(CH₂)_(a)-heteroaryl; and, R⁴ is hydrogen, alkyl, substituted alkyl,—(CH₂)_(a)-aryl or —(CH₂)_(a)-heteroaryl; wherein a is an integer from 0to about 6.

In an exemplary embodiment, the nucleic aid reporter molecule of thepresent kits have the formula:

-   -   or the formula

In this instance, each R^(1a) and R^(1b) are independently hydrogen,carboxy, sulfo, phosphate, phosphonate, amino, hydroxyl,trifluoromethyl, halogen, alkyl, substituted alkyl, alkoxy, alkylamino,substituted alkylamino, dialkylamino, substituted dialkylamino, fusedbenzene, substituted fused benzene, trifluomethyl, halogen, reactivegroup, solid support or carrier molecule. t is an integer from 0 toabout 4.

In one aspect R⁴ is hydrogen, alkyl, —(CH₂)_(a)-aryl, or—(CH₂)_(a)-heteroaryl, wherein a is an integer from 0 to about 6. In afurther aspect R⁴ is an alkyl, phenyl, benzyl, alkylthio, indolyl,imidazolyl, or thiazolyl. Typically at least one of R¹ and R² comprisesa negatively charged substituent. An exemplified nucleic acid reportermolecule is Compound 25.

In an exemplary embodiment, the nucleic aid reporter molecule of thepresent kits comprise a reactive group, solid support and carriermolecule wherein these substituents independently comprise a linker thatis a single covalent bond, or a covalent linkage that is linear orbranched, cyclic or heterocyclic, saturated or unsaturated, having 1-20nonhydrogen atoms selected from the group consisting of C, N, P, O andS; and are composed of any combination of ether, thioether, amine,ester, carboxamide, sulfonamide, hydrazide bonds and aromatic orheteroaromatic bonds.

In an exemplary embodiment, the reactive group is selected from thegroup consisting of an acrylamide, an activated ester of a carboxylicacid, a carboxylic ester, an acyl azide, an acyl nitrile, an aldehyde,an alkyl halide, an anhydride, an aniline, an amine, an aryl halide, anazide, an aziridine, a boronate, a diazoalkane, a haloacetamide, ahaloalkyl, a halotriazine, a hydrazine, an imido ester, an isocyanate,an isothiocyanate, a maleimide, a phosphoramidite, a reactive platinumcomplex, a silyl halide, a sulfonyl halide, a thiol and aphotoactivatable group. In a further aspect, the reactive group isselected from the group consisting of carboxylic acid, succinimidylester of a carboxylic acid, hydrazide, amine and a maleimide.

In an exemplary embodiment the carrier molecule is selected from thegroup consisting of an amino acid, a peptide, a protein, apolysaccharide, a nucleoside, a nucleotide, an oligonucleotide, anucleic acid polymer, a hapten, a psoralen, a drug, a hormone, a lipid,a lipid assembly, a synthetic polymer, a polymeric microparticle, abiological cell or a virus. In a further aspect, the carrier molecule isselected from the group consisting of an antibody or fragment thereof,an avidin or streptavidin, a biotin, a blood component protein, adextran, an enzyme, an enzyme inhibitor, a hormone, an IgG bindingprotein, a fluorescent protein, a growth factor, a lectin, alipopolysaccharide, a microorganism, a metal binding protein, a metalchelating moiety, a non-biological microparticle, a peptide toxin, aphosphotidylserine-binding protein, a structural protein, asmall-molecule drug, or a tyramide.

In an exemplary embodiment, the solid support is selected from the groupconsisting of a microfluidic chip, a silicon chip, a microscope slide, amicroplate well, silica gels, polymeric membranes, particles,derivatized plastic films, glass beads, cotton, plastic beads, aluminagels, polysaccharides, polyvinylchloride, polypropylene, polyethylene,nylon, latex bead, magnetic bead, paramagnetic bead, andsuperparamagnetic bead. In a further aspect, the solid support isselected from the group consisting of Sepharose, poly(acrylate),polystyrene, poly(acrylamide), polyol, agarose, agar, cellulose,dextran, starch, FICOLL, heparin, glycogen, amylopectin, mannan, inulin,nitrocellulose, diazocellulose and starch.

A detailed description of the invention having been provided above, thefollowing examples are given for the purpose of illustrating theinvention and shall not be construed as being a limitation on the scopeof the invention or claims.

EXAMPLES Example 1 Preparation of Compound 1

A mixture of 12.4 g of 3-(2-benzothiazolylthio)-1-propanesulfonic acid,sodium salt and 14.6 g of propanesultone is heated in 40 mL of DMF atreflux for 6 hours. The crude mixture is added slowly to 40 mL of ethylacetate and stirred for three days. The solid product is filtered,redissolved in 100 mL of water, and lyophilized to obtain Compound 1.

Example 2 Preparation of Compound 2

To 0.235 g of 4-methyl-1-phenyl-quinolin-2-one in 10 mL of THF at −78°C. under nitrogen, 1 mL of 2.5 M n-Butyllithium is introduced. Afterstirring for 30 minutes, 0.5 mL of acetic acid is added and theresulting mixture is further stirred at room temperature. All volatilecomponents are then removed under reduced pressure to yield the crude2-butyl-4-methyl-1-phenylquinolinium intermediate. This intermediate isthen dissolved in 5 mL of methanol and added to a slurry of 0.82 g ofCompound 1 in 15 mL of methanol, with the subsequent addition of 0.56 mLof triethylamine. The resulting mixture immediately turns red. Afterseveral hours of stirring at room temperature, the solvent is evaporatedand the crude product is purified using silica gel columnchromatography.

The following compounds (3-19) are prepared using methods analogous tothose used above to prepare Compound 2. For example, excess3-(3-sulfoproypyl)-2-(3-sulfopropylthio)-benzthiazolium, inner salt maybe reacted with the corresponding appropriate quinolinium moiety in thepresence of a base (e.g. triethylamine) to generate Compounds 3-19.

TABLE 3 Fluorescence Enhancement Ex/Em Ratio Compound (nm)¹ (DNA/RNA)²

500/520 6.8

507/550 6.1

505/530 4.5

524/555 17

521/555 17

520/556 18.5

500/525 3.8

522/570 5.9

527/560 4.3

507/545 3.2

523/566 3.6

520/556 5.8

525/565 12.6

524/557 38

505/531 6.2

524/603 2.6

505/551 7.9

504/531 1.3 ¹Complex with nucleic acid ²The ratio of the fluorescenceenhancement of the compound when associated with DNA to the fluorescenceenhancement of the compound when associated with RNA

Example 3 Preparation of Compound 20

To 50 mL of chlorosulfonic acid at room temperature is added 10 g of2-methylthio-benzothiazole in small portions. After the addition iscomplete, the reaction mixture is heated at 35° C. for several hours.The reaction mixture is then cooled to room temperature and addeddropwise to 750 mL of an ice/water slurry with vigorous stirring. Theresulting white solid product is collected by filtration, stirred in 200mL of water for 30 minutes, and filtered again to recover 14.5 g ofCompound 20.

Example 4 Preparation of Compound 21

To about 8 g of the sulfonyl chloride Compound 20 in 80 mL of water isadded 10 mL of a 10% NaOH solution. The resulting mixture is stirred atroom temperature overnight. The resulting solid is filtered, stirred in100 mL of methanol for 4 hours and 2.5 g of Compound 21 is recovered.

Example 5 Preparation of Compound 22

A mixture of 0.6 g of Compound 21 and 1.9 g of methyl toluenesulfonateis heated in 4 mL of DMF at 120° C. for 1 hour. Ethyl acetate (20 mL) isthen added, and the resulting mixture heated at reflux for an additional5 minutes. The product (1.67 g) Compound 22 is recovered by filtrationas a white solid.

Example 6 Preparation of Compound 23

To a mixture of 0.92 mmole of Compound 22 and 1 mmole of1,4-dimethyl-2-(2-(1-methylimidazolyl)-quinolinium acetate in 5 mL ofmethanol is added 0.6 mL of triethylamine. The reaction mixture isstirred for an hour, and the resulting dark red solid is collected byfiltration. The product thus obtained is washed with methanol and driedto give Compound 23.

The following compounds (24-28) may be prepared in a method analogous tothat of Compound 23, above. For example, excess Compound 22 may bereacted with the appropriate quinolinum/pyridinium moiety in thepresence of a base (e.g. triethylamine) to generate the desired product.

Table 4 below shows the differential fluorescence enhancement ofselected compounds when associated with DNA, when compared to theirfluorescent enhancement when associated with RNA.

TABLE 4 Fluorescence Enhancement Ex/Em Ratio Compound (nm)¹ (DNA/RNA)²

519/552 9

498/522 6.6

504/522 26

522/554 47

447/483 4.1

501/NA NA

504/522 1

447/483 1 ¹Complex with nucleic acid ²The ratio of the fluorescenceenhancement of the compound when associated with DNA to the fluorescenceenhancement of the compound when associated with RNA ³Included forcomparison purposes

Example 7 Preparation of Compound 31

To a mixture of 0.28 g of 4-methyl-1-(4-sulfobutyl)-quinolinium, innersalt and 0.367 g of 3-methyl-2-methylthio-benzothiazolium tosylate in 15mL of dichloromethane is added 0.16 mL of triethylamine. The reactionmixture is stirred at room temperature overnight. The crude product isrecovered by filtration and stirred in 20 mL of 1:1 (v/v) mixture of DMFand acetonitrile for 30 minutes to obtain Compound 31.

Example 8 Preparation of Compound 32

A mixture of 55 mg of 3-(3-sulfopropyl)-2-methylbenzothiazolium, innersalt and 78 mg of 4-chloro-1-methylquinolinium tosylate and 0.07 mL oftriethylamine is stirred in 10 mL of dichloromethane at room temperatureovernight. The resulting product is recovered from filtration to giveCompound 32.

Example 9 Preparation of Compound 33

To a mixture of 0.1 g of Compound 41 and 1-benzyl-4-chloroquinoliniumbromide in 10 mL of dichloroethane is added 0.22 mL of triethylamine andthe reaction mixture is stirred for several hours. The reaction mixtureis then diluted with chloroform and washed with brine, and the crudeproduct thus obtained is purified using silica gel column chromatographyto yield pure Compound 33.

Example 10 Preparation of Compound 34

To a suspension of 0.5 g of the sulfonyl chloride Compound 20 in 10 mLof water, 0.47 g of 6-aminohexanoic acid and 2.5 mL of 10% NaOH areintroduced and the mixture is stirred at room temperature overnight. Thesolvent is removed by evaporation, and the crude product is purifiedusing silica gel column chromatography to give compound 34.

Example 11 Preparation of Compound 35

A mixture of 0.381 g of the carboxylic acid derivative Compound 34 and0.23 g of methyl toluenesulfonate is heated at 120° C. for 1.5 hours.Ethyl acetate (about 30 mL) is added and the mixture briefly heated atreflux. The resulting product is obtained via filtration to giveCompound 35.

Example 12 Preparation of Compound 36

0.1 mL of triethylamine is added to a mixture of 0.13 g of Compound 35and 80 mg of 1-benzyl-4-methylquinolinium bromide in a mixed solventsystem of 10 mL dichloroethane and 3 mL of DMF. The resulting mixture isstirred at room temperature overnight. The resulting product is filteredand further purified by stirring in 2 mL of methanol for 30 minutes togive Compound 36.

Example 13 Preparation of Compound 37

A mixture of 1.49 g of 2-methylbenzothiazole and 1.63 g of butanesultoneis heated at 130° C. for 1.5 hours. Ethyl acetate (40 mL) is added andthe resulting mixture heated at reflux for minutes. The resultingproduct is collected by filtration to give Compound 37.

Example 14 Preparation of Compound 38

To 57 mg of Compound 37 and 84 mg of 4-chloro-1-methylquinoliniumtosylate in 10 mL of dichloromethane is added 0.07 mL of triethylamine.The reaction mixture is stirred at room temperature overnight andCompound 38 is obtained via filtration.

Example 15 Preparation of Compound 39

A mixture of 2.66 g of 2-methylbenzoxazole and 2.68 g of propanesultoneis heated at 150° C. for 1 hour. Ethyl acetate (30 mL) is added and theresulting mixture is heated at reflux for 1 hour. Compound 39 isrecovered via filtration.

Example 16 Preparation of Compound 40

To a mixture of 0.1 g of Compound 39 and 0.15 g of4-chloro-1-methylquinolinium tosylate in 10 mL of dichloromethane isadded 0.1 mL of triethylamine and the resulting reaction mixture isstirred at room temperature overnight. The volatile components areremoved by evaporation under reduced pressure and the resulting residueis stirred in 2 mL of methanol and filtered to obtain Compound 40.

Example 17 Preparation of Compound 41

A mixture of 1.49 g of 2-methylbenzothiazole and 2 g of 4-bromobutyricacid is heated at 150° C. for 1 hour. Ethyl acetate (30 mL) is added andthe mixture is heated at reflux for 30 minutes. Compound 41 is obtainedvia filtration.

Example 18 Preparation of Compound 42

To a mixture of 0.12 g of Compound 41 and 0.146 g of4-chloro-1-methylquinolinium tosylate in 10 mL of dichloromethane isadded 0.1 mL of triethylamine, and the reaction mixture is stirredovernight. Compound 42 is obtained via filtration.

Example 19 Preparation of Compound 43

A mixture of 3 g of 2-methylbenzothiazole and 2.11 g of2-bromoethanesulfonic acid, sodium salt is heated at 130-140° C. for 8hours, after which 0.12 g of 4-chloro-1-methylquinolinium tosylate isadded. The resulting mixture is stirred in 15 mL of methanol and 0.5 mLof triethylamine is added. The reaction mixture is stirred at roomtemperature overnight and Compound 43 is purified using silica gelchromatography.

Example 20 Preparation of Compound 44

A mixture of 20 mg of 2-methyl-oxazolo[4,5-b]pyridine and 36 mg ofpropanesultone is heated in 0.1 mL of DMF at 140° C. for 20 minutes.After cooling to room temperature, 2 mL of ethyl acetate is added andthe supernatant solution is decanted. To the crude intermediate2-methyl-4-(3-sulfopropyl)-oxazolo[4,5-b]pyridinium inner salt is added1.5 mL of DMF, followed by 33 mg of 4-chloro-1-methylquinoliniumtosylate and 0.05 mL of triethylamine. The crude product is thenpurified using silica gel chromatography to give Compound 44.

Example 21 Preparation of Compound 45

To a mixture of 0.38 g of the sulfonyl chloride derivative Compound 20and 0.3 g of 5-((2-aminoethyl)amino)naphthalene-1-sulfonic acid, sodiumsalt in about 5 mL of DMF is added 0.31 mL of triethylamined and theresulting reaction mixture is stirred at room temperature for severalhours. The solvent is removed by evaporation under reduced pressure andthe crude product is purified using silica gel column chromatography toyield 0.16 g of Compound 45.

Example 22 Preparation of Compound 46

A mixture of 18 mg of the sulfonic acid sodium salt derivative Compound45 and 200 mg of methyl toluenesulfonate is stirred at 130° C. for 15minutes. After cooling down to room temperature, the crude product iswashed with 4 mL of ethyl acetate, centrifuged and decanted. Theresulting residue is dissolved in 0.5 mL of DMF and 20 mg of1-benzyl-4-methylquinolinium bromide and 0.07 mL of triethylamine areintroduced in that order. Compound 46 is then isolate using silica gelchromatography.

Example 23 Preparation of Compound 47

To a mixture of 0.25 g of the sulfonyl chloride Compound 20 and 0.25 gof 3-aminopropylphosphonic acid in 10 mL of water at room temperature, 1mL of 10% NaOH is added and stirred at ambient temperature overnight.The water is evaporated and the crude product is purified on silica gelcolumn to give Compound 47.

Example 24 Preparation of Compound 48

A mixture of about 5 mg of the phosphonic acid derivative Compound 47and 4-5 equivalents of methyl toluenesulfonate is heated at 130° C. for1 hour. Ethyl acetate (2 mL) is added and the suspension is centrifugedand decanted. The residue is then dissolved in about 0.5 mL of DMF andtreated with about 25 mg of 1,4-dimethylquinolinium iodide and 0.1 mL oftriethylamine and the resulting mixture is stirred for several hours.The solvent is evaporated under reduced pressure and Compound 48 ispurified on silica gel.

Example 25 Preparation of Compound 54

A mixture of 25 mg of6-(methoxycarbonyl)-3-methyl-2-methylthio-benzothiazolium tosylate and20 mg of 1-benzyl-4-methylquinolinium bromide and 0.03 mL oftriethylamine is stirred in 1 mL of dichloroethane at room temperaturefor 2 hours. Several millilters of chloroform are introduced andpartitioned with several milliliters of water. The intermediate methylester of the desired product is collected by filtration, and thenhydrolyzed by aqueous sodium hydroxide in methanol to generate theproduct, Compound 54.

Example 26 Preparation of Compound 49

A mixture of 0.3 g of the bis-sulfonic acid derivative Compound 1, 94 mgof 1,4-dimethylpyridinium iodide and 0.14 mL of triethylamine in 10 mLof methanol is stirred at room temperature for one hour. The crudeproduct is then purified on silica gel to give Compound 49.

Example 27 Preparation of Compound 50

To a mixture of about 0.4 mmole of2-(4-aminophenylthio)-4-methyl-1-phenylquinolinium chloride and 0.39 gof Compound 1 in 5 mL of methanol is added 0.21 mL of triethylamine, andthe resulting mixture is stirred at room temperature for 2 hours. Thecrude product is then purified on a silica gel column to give Compound50.

Example 28 Preparation of Compound 51

Compound 51 is made following a procedure similar to the preparation ofCompound 50 (see Example 27) excepting that2-(3,5-dimethylphenylthio)-4-methyl-1-phenylquinolinium chloride is usedinstead of 2-(4-aminophenylthio)-4-methyl-1-phenylquinolinium chloride.The crude product is purified on a silica gel column to give Compound51.

Example 29 Preparation of Compound 52

Compound 52 is made following a procedure similar to the preparation ofCompound 50 (see Example 27) excepting that2-(4,6-dimethylpyrimidinyl-2-thio)-4-methyl-1-phenylquinolinium chlorideis used instead of 2-(4-aminophenylthio)-4-methyl-1-phenylquinoliniumchloride. The crude product is purified on a silica gel column to giveCompound 52.

Example 30 Preparation of Compound 53

A mixture of 0.46 g of the bis-sulfonic acid derivative Compound 1,0.165 g of 1,2-dimethylquinolinium tosylate and 0.14 mL of triethylaminein 10 mL of methanol is stirred at room temperature for two hours. Thecrude product is purified on silica gel to give Compound 53.

Example 31 Emission Spectra of Compound 25 in the Presence of DNA andRNA Demonstrating Brighter Fluorescent Signal from DNA

A stock solution of Compound 25 is made by dissolving about 0.1 to about0.3 mg of the reporter molecule in 1 mL of DMSO. The stock solution (40μl) is then diluted in 3 ml 10 mM TRIS, 1 mM EDTA (pH 7.2). This dilutesolution resulted in an optical density of approximately 0.058 andextinction coefficient of 45,000, yielding a working concentration of˜2.9-8.8 μM. Compound 25, at about 2.9-8.8 μM, is added to the testsamples (1)_(r)RNA and 2) DNA calf thymus. The RNA is present at a finalconcentration of 65 μg/ml and the DNA is present at a finalconcentration of about 66 μg/mL. After addition of the dye and thenucleic acid, the samples are incubated at room temperature for about 30minutes, then excited at 504 nm and the resulting emission detected at522 nm. Compound 25 demonstrates a 600-fold increase in fluorescencesignal when bound to DNA when compared to the corresponding RNA complex,as shown in FIG. 1.

This example provides a means for screening reporter compounds for theirability to fluoresce when complexed with DNA or RNA. In addition, thismethodology provides a means for screening compounds wherein aparticular intensity is desired or compounds that are selective for DNAand/or RNA.

Table 5 below shows the differential fluorescence enhancement ofselected compounds when associated with DNA, when compared to theirfluorescent enhancement when associated with RNA.

TABLE 5 DNA-selective compounds Fluorescence Ex/Em Enhancement RatioCompound (nm)¹ (DNA/RNA)² Compound 31 503/529 1.6 Compound 32 509/5264.3 Compound 33 507/532 4.2 Compound 36 502/524 9.2 Compound 38 502/5302.8 Compound 40 475/503 2.3 Compound 42 502/526 3.3 Compound 43 499/5252.7 Compound 44 520/545 1.3 Compound 46 501/525 3.2 Compound 48 496/5202.7 Compound 54 508/532 7.4 Thiazole 510/530 1.0 Orange³ ¹Complex withnucleic acid ²The ratio of the fluorescence enhancement of the compoundwhen associated with DNA to the fluorescence enhancement of the compoundwhen associated with RNA ³Included for comparison purposes

Table 6 below shows the differential fluorescence enhancement ofselected compounds when associated with RNA, when compared to theirfluorescent enhancement when associated with DNA.

TABLE 6 RNA-selective compounds Fluorescence Ex/Em Enhancement RatioCompound (nm)¹ (RNA/DNA)² Compound 49 444/480 2.2 Compound 50 508/5403.3 Compound 51 508/540 2.6 Compound 52 517/555 1.2 Compound 53 480/5301.5 Thiazole 510/530 1.0 Orange³ ¹Complex with nucleic acid ²The ratioof the fluorescence enhancement of the compound when associated with RNAto the fluorescence enhancement of the compound when associated with DNA³Included for comparison purposes

Example 32 Comparison of In-Solution Binding of Compound 25 with RNA orDNA

A buffer solution of 200 μl of 10 mM TRIS, 1 mM EDTA (pH7.2) is added tothe wells of a 96-well microplate. RNA and DNA (calf thymus) dilutionsin TE (pH 7.2) are added to the appropriate wells to yield the finalconcentrations of 0-10,000 ng/mL. Compound 25, prepared from a stocksolution in DMSO, is added to the microplate wells to a finalconcentration of 2 μM. The well contents are excited at 504 nm andemission is recorded at 522 nm. Compound 25 demonstrated an increasedfluorescence intensity signal with increasing concentrations of DNA, butexhibited little to no fluorescence signal when combined with RNA alone,as shown in FIG. 2. This experimental provides a means for screeningpotential reporter molecules that may selectively bind DNA or RNA.

Example 33 Comparison of In-Solution Binding of Compound 25 to DNA, RNAor a 1:1 Ratio of RNA and DNA

A buffer solution of 200 μl of 10 mM TRIS, 1 mM EDTA (pH 7.2) is addedto the wells of a 96-well microplate. RNA and DNA (calf thymus)dilutions in TE (pH 7.2) are added to the appropriate wells to yieldfinal concentrations of 0-4000 ng/mL. In separate wells RNA and DNA arecombined for a final concentration of 800, 1600, 2400, 3200 and 4000ng/mL of nucleic acid. Compound 25, from a stock solution in DMSO, isadded to the microplate wells at a final concentration of 2.0 μM. Thewell contents are excited at 504 nm and emission is recorded at 522 nm.Compound 25 demonstrates selectivity for DNA, as shown in FIG. 3.

FIG. 3 represents an overlay of three graphs with concentration of DNA0-4000 ng/mL, RNA 0-4000 ng/mL (along the same axis) and RNA+DNA. Thecombined concentration is always twice the concentration of nucleic acidindicated on the X-axis such that the individual concentration of RNAand DNA depends on the corresponding concentration indicated on theX-axis. In this way the concentrations were combined in the followingformat: RNA+DNA respectively, 0 ng/mL+0 ng/mL, 800 ng/mL+800 ng/mL, 1600ng/mL+1600 ng/mL, 2400 ng/mL+2400 ng/mL, 3200 ng/mL+3200 ng/mL, and 4000ng/mL+4000 ng/mL. Compound 25 either does not bind RNA, or binds RNAwith little to no fluorescent signal intensity which is confirmed by thefluorescence response in the presence of RNA and DNA as is observed forthe corresponding DNA concentration alone.

This experiment provides a means for screening present reportermolecules for their ability to detect RNA in the presence of DNA, oralternatively for their ability to detect DNA in the presence of RNA

Example 34 Comparison of in Solution Binding of Compound 25 to DNA, RNAor a Mixture of DNA and RNA wherein the Concentration of DNA isconstant.

A buffer solution of 200 μl of 10 mM TRIS, 1 mM EDTA (pH 7.2) is addedto the wells of a 96-well microplate. RNA and DNA (calf thymus)dilutions in TE (pH 7.2) are added to the appropriate wells to yield thefinal concentrations of 0-4000 ng/mL. DNA (1 μg/ml) is added to varyingamounts of RNA (0, 800, 1600, 2400, 3200 and 4000 ng/ml) in TE bufferand added to appropriate wells. Compound 25, from a stock solution inDMSO, is added to the microplate wells to a final concentration of 2.0μM. The well contents are excited at 504 nm and emission is recorded at522 nm. Compound 25 demonstrates selectivity for DNA, as shown in FIG.4.

FIG. 4 is an overlay of two graphs showing fluorescence response due toincreasing concentrations of DNA only (0-4000 ng/ml), and fluorescenceresponse due to increasing concentrations of RNA (0-4000 ng/ml) in thepresence of a constant concentration of DNA (1000 ng/ml). The resultsindicate that Compound 25 demonstrates an ability to selectivelyassociate with DNA in the presence of varying concentrations of RNA,that at equal concentrations of RNA and DNA, DNA may be effectivelydetected using Compound 25, and that Compound 25 may still effectivelydetect DNA when the concentration of RNA is four times the concentrationof DNA.

Example 35 Titration of DNA and RNA in the Presence of Compound 25

A buffer solution of 200 μl of 10 mM TRIS, 1 mM EDTA (pH 7.2) is addedto the wells of a 96-well microplate. RNA and DNA (calf thymus)dilutions in TE (pH 7.2) are added to the appropriate wells to yield thefinal concentrations of 0-10,000 ng/mL. Compound 25, from a stocksolution in DMSO, is added to the microplate wells to a finalconcentration of 1.0, 1.5 and 2.0 μM. The well contents are excited at504 nm and emission is recorded at 522 nm. Compound 25 demonstrates aselectivity for DNA with optimal signal when Compound 25 is present at2.0 μM, as shown in FIG. 5.

Example 36 Detection of dsDNA and ssDNA Spotted on a Microarray

Selectivity for dsDNA

A microarray including a dilution series of plasmid DNA is printed inquadruplicate using a microarray spotter. The dilution series includesspots of about 200 pg to about 1 pg of plasmid DNA printed from either50% DMSO/50% H₂O (in order to denature the DNA and render itpredominantly single stranded) or 3× SSC (in order to retaindouble-strandedness). The slide including the printed microarray isequilibrated in a salt buffer to remove any excess printing buffer, andthen soaked in a 1 μM solution of Compound 5 in a salt buffer for 5minutes, followed by a 5 minute wash in a salt buffer to remove anyexcess stain. The slide is then imaged by a microarray scanner using 633nm laser excitation. The resulting false color image clearly indicatesthat the top row of single-stranded DNA is stained to a lesser degreewhen compared to the corresponding dilution series of double-strandedDNA, as shown in FIG. 6. This suggests that Compound 5 exhibits higheraffinity for double-stranded nucleic acids than for single-strandednucleic acids when immobilized on solid supports.

Example 37 Detection of Hybridized and dsDNA and ssDNA Spotted on aMicroarray

Selectivity for Hybridized DNA

Dilution series of plasmid DNA One (rows 1 and 2, about 100 pg to about10 fg), plasmid DNA Two (rows 3 and 4, about 10 pg to about 1 fg), andplasmid DNA Three (rows 5 and 6, about 30 pg to about 3 fg),respectively, are printed from 50% DMSO/50% H2O onto a slide using amicroarray spotter. The solvent is selected so as to denature the DNAand render it predominantly single-stranded on the slide.

The slide is then hybridized with a fluorescent-labeled (ALEXA FLUOR 488dye) probe following standard hybridization conditions. The slide issoaked in a staining solution of Compound 5 (about 1 μM) in a saltbuffer for 5 minutes, followed by a 1-minute wash in a salt buffer toremove any excess stain. The slide is then imaged with a microarrayscanner using 488 nm laser excitation (as shown in FIG. 7), and 633 nmlaser excitation (as shown in FIG. 8).

Illumination at 488 nm reveals the presence of the fluorescent-labeledprobe, and indicates that the probe hybridizes to DNA that is 100%complementary (middle rows 3 and 4) and partially complimentary (toprows 1 and 2), but does not hybridize to the non-complimentary bottomtwo rows 5 and 6, as shown in FIG. 7. Illumination at 633 nm reveals DNAstained by Compound 5, and as shown in FIG. 8, staining reveals similarpattern as is generated by the hybridization probe. That is, Compound 5has a higher affinity for staining hybridized DNA, when compared tounhybridized single-stranded DNA.

The preceding examples can be repeated with similar success bysubstituting the specifically described nucleic acid reporter moleculesof the preceding examples with those generically and specificallydescribed in the forgoing description. One skilled in the art can easilyascertain the essential characteristics of the present invention, andwithout departing from the spirit and scope thereof, can make variouschanges and modifications of the invention to adapt to various usagesand conditions.

All patents and patent applications mentioned in this specification areherein incorporated by reference to the same extent as if eachindividual patent or patent application was specifically andindividually indicated to be incorporated by reference.

1. A method for detecting DNA in the presence of RNA, wherein the method comprises the steps: a. combining a nucleic acid reporter molecule with a sample to prepare a labeling mixture, wherein the nucleic acid reporter molecule has a DNA/RNA ratio of fluorescence enhancement greater than about one wherein the nucleic acid reporter molecule is according to the formula

wherein W represents the atoms necessary to form one or two fused substituted 5- or 6-membered aromatic rings or one or two unsubstituted 5- or 6-membered aromatic rings; R² is a substituted alkyl, unsubstituted alkyl, substituted arylalkyl, unsubstituted arylalkyl, substituted heteroalkyl, unsubstituted heteroalkyl, alkoxy, carboxy, carboxyalkyl, hydroxy, hydroxyalkyl, sulfo, sulfoalkyl, amino, aminoalkyl, alkylamino, dialkylamino, or trialkylammonium; α is 0 or 1; n is 0 or 1; X is O, S, or Se; D is a substituted pyridinium, unsubstituted pyridinium, substituted quinolinium, or unsubstituted quinolinium moiety; with the proviso that the compound is substituted by at least one negatively charged moiety at a physiological pH; b. incubating the labeling mixture for a sufficient amount of time for the nucleic acid reporter molecule to associate with DNA in the sample to form an incubated mixture; c. illuminating the incubated mixture with an appropriate wavelength to form an illuminated mixture; and, d. observing the illuminated mixture whereby the DNA is detected in the presence of RNA.
 2. The method according to claim 1, further comprising quantifying the DNA present in the sample.
 3. The method according to claim 1, wherein the sample comprises biological fluids, buffer solutions, live cells, fixed cells, eukaryotic cells, prokaryotic cells, nucleic acid polymers, nucleotides, nucleosides, a polymeric gel or tissue sections.
 4. The method according to claim 1, wherein the sample comprises cells, tissue, or biological fluids.
 5. The method according to claim 1, wherein the sample is present in or on a microarray or a microwell plate. 